Diversity

20 pages, 3024 KiB

Open AccessArticle

Assessing the Effects of Phytoplankton Structure on Zooplankton Communities in Different Types of Urban Lakes

by Larisa I. Florescu, Mirela M. Moldoveanu, Rodica D. Catană, Ioan Păceșilă, Alina Dumitrache, Athanasios A. Gavrilidis and Cristian I. Iojă

Diversity 2022, 14(3), 231; https://doi.org/10.3390/d14030231 - 21 Mar 2022

Cited by 16 | Viewed by 4007

Abstract

Urban lakes play important roles in microclimate regulation such as controlling run-off and groundwater recharge, as well as being a source of water supply and a habitat for a wide variety of flora and fauna. Bucharest has a wide variety of water resources [...] Read more.

Urban lakes play important roles in microclimate regulation such as controlling run-off and groundwater recharge, as well as being a source of water supply and a habitat for a wide variety of flora and fauna. Bucharest has a wide variety of water resources where phytoplankton represent the dominant primary producer, the defining biological factor for zooplankton development. Our hypothesis was that as a result of anthropogenic pressures, phytoplankton in the urban aquatic ecosystems diminish the qualitative and quantitative capacity to maintain a good health condition with effects on the food web. By the structural features of the phytoplankton and zooplankton communities, the objectives were to determine the changes in diversity in different types of urban lakes, to explore the relationships between communities, and to determine the response of phytoplankton and zooplankton functional groups to the environmental factors. The ecological status assessed by Chlorophyll-a (µL⁻¹) highlights that most of the investigated lakes were eutrophic and hypereutrophic. The phytoplankton were influenced by lake types, seasonal variations and nutrient input. The dominance of the Chlorophyceae, Cyanobacteria and Bacillariophyceae influenced the zooplankton’s development. The rotifers were the most represented in both species richness and abundance in zooplankton, followed by Copepoda young stages. Full article

(This article belongs to the Special Issue Biological Diversity of Freshwater Invertebrates)

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16 pages, 6504 KiB

Open AccessArticle

Contrasting Impact of Viral Activity on Prokaryotic Populations in the Coastal and Offshore Regions of the Eastern Arabian Sea

by PK Shruthi, Ammini Parvathi, Angia Sriram Pradeep Ram, Shyla Hafza, Jose K. Albin, Erathodi Rajagopalan Vignesh, Jaleel Abdul and Telesphore Sime-Ngando

Diversity 2022, 14(3), 230; https://doi.org/10.3390/d14030230 - 21 Mar 2022

Cited by 2 | Viewed by 2830

Abstract

Viral processes in the coastal and offshore regions of the Eastern Arabian Sea (west coast of India) and their contribution of viral lysis to the organic carbon and nitrogen pool was examined. Water samples were collected during the southwest monsoon season at different [...] Read more.

Viral processes in the coastal and offshore regions of the Eastern Arabian Sea (west coast of India) and their contribution of viral lysis to the organic carbon and nitrogen pool was examined. Water samples were collected during the southwest monsoon season at different depths (up to 1000 m) from four transects, with each transect consisting of two sampling points (S1–S8). Abundances of viruses and prokaryotes together with viral mediated prokaryotic mortality (up to 49.7%) were significantly (p < 0.001) higher in eutrophic coastal stations, whereas high percent lysogeny (up to 93%) was observed in the offshore regions. High viral-mediated carbon (Mean ± SD = 67.47 ± 2.0 μM C L⁻¹ d⁻¹) and nitrogen (Mean ± SD = 13.49 ± 14.0 μM N L⁻¹ d⁻¹) release was evident in the surface coastal waters compared to offshore regions. The percentage contributions of carbon and nitrogen released by viral lysis to the total dissolved organic carbon and nitrogen pool were estimated to be 7.4% and 3.9%, respectively, in the coastal surface waters. Our findings suggest that the contribution of viral lysis to DOM production through viral shunt could be crucial for the cycling of major biogeochemical elements and functioning of the studied tropical ecosystem. Full article

(This article belongs to the Special Issue Ecology of Microbes in Marine and Estuarine Ecosystems)

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23 pages, 8595 KiB

Open AccessEditor’s ChoiceArticle

Impact of Invasive Weeds on the Diversity and Dissimilarity of Bird Communities in Forested Areas

by Emilia Grzędzicka

Diversity 2022, 14(3), 229; https://doi.org/10.3390/d14030229 - 20 Mar 2022

Cited by 5 | Viewed by 3341

Abstract

Caucasian hogweeds, mainly the Sosnowsky’s hogweed Heracleum sosnowskyi and the giant hogweed Heracleum mantegazzianum, create one of the most problematic plant invasions in the world. Due to their large size (weeds reaching 4–5 meters in height), they seem to be herbaceous plants [...] Read more.

Caucasian hogweeds, mainly the Sosnowsky’s hogweed Heracleum sosnowskyi and the giant hogweed Heracleum mantegazzianum, create one of the most problematic plant invasions in the world. Due to their large size (weeds reaching 4–5 meters in height), they seem to be herbaceous plants that can threaten birds living in forest stands. This research quantified the structure and diversity of the forest birds’ community in forests with varying areas of invasive hogweeds located in south-eastern Poland. Changes in the accompanying non-forest birds’ community were also assessed. The study addressed the following questions: 1. How does the invaded area correlate with the abundance of forest birds? 2. How do communities and species respond to invaded vegetation? 3. How do the invading plants affect the various types of diversity of forest and non-forest birds? It turned out that both surveyed bird communities had a lower alpha diversity in invaded sites. Only forest birds, not able to change their location easily, formed a unique community (i.e., had a higher beta diversity) near invaders. Forest birds showed unchanged functional diversity based on the relative bird abundance and their connection, or lack of it, with the forest development phases. The effect of hogweeds on the abundance of forest birds was more negative in severely invaded areas with anthropogenic habitats. Non-forest birds showed higher species loss near the invasion, constant beta diversity and decreased functional diversity. This study is important as the forest is a climax community in the temperate zone, and unused open areas become spontaneously overgrown with young forests. Weeds disseminating after crop abandonment can highly and commonly affect forest and non-forest bird communities co-occurring in this type of overgrowing area. Full article

(This article belongs to the Special Issue Birds in Temperate and Tropical Forests)

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20 pages, 8019 KiB

Open AccessArticle

Comprehensive Genomic Analysis of G2-like Transcription Factor Genes and Their Role in Development and Abiotic Stresses in Arabidopsis

by Intikhab Alam, Xueting Wu, Qianxia Yu and Liangfa Ge

Diversity 2022, 14(3), 228; https://doi.org/10.3390/d14030228 - 20 Mar 2022

Cited by 12 | Viewed by 3987

Abstract

GOLDEN2-LIKE (GLK) transcription factors are a subfamily of GARP family transcription factors, which play an essential function in plant growth and development as well as stress response during abiotic and biotic stress conditions. This study reports GLK genes in the Arabidopsis thaliana genome [...] Read more.

GOLDEN2-LIKE (GLK) transcription factors are a subfamily of GARP family transcription factors, which play an essential function in plant growth and development as well as stress response during abiotic and biotic stress conditions. This study reports GLK genes in the Arabidopsis thaliana genome in-depth and identified 55 AtGLK genes in the Arabidopsis genome. Phylogenetic analyses resolved these GLK gene clusters into seven groups. A Ka/Ks ratios analysis indicated that they had experienced purifying selection. Many essential cis elements are present in the promoter regions of AtGLK genes associated with plant hormones, light, and stress. The expression profile from RNA-Seq data revealed that 29.1% of them had relatively high expression in all tested tissues or organs, indicating their crucial housekeeping function in plant growth and development. However, many other GLK members were selectively expressed in particular tissues or organs. In silico study of the transcriptional regulation of AtGLKs indicated that it is strongly regulated by cold, drought, osmotic, salt, and metal ion stressors. Our research provides essential information for the functional studies of each GLK gene in different species in the future. Full article

(This article belongs to the Special Issue Generation of Genome-Wide Genetic Data and Evolutionary Analyses)

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13 pages, 1604 KiB

Open AccessArticle

The Importance of Forest Elephants for Vegetation Structure Modification and Its Influence on the Bird Community of a Mid-Elevation Forest on Mount Cameroon, West-Central Africa

by Solange Mekuate Kamga, Simon Awafor Tamungang, Taku Awa II, Francis Luma Ewome, Francis Njie Motombi, David Hořák and Jan Riegert

Diversity 2022, 14(3), 227; https://doi.org/10.3390/d14030227 - 19 Mar 2022

Cited by 4 | Viewed by 4151

Abstract

Most of the tropical rainforests are subject to both anthropogenic and natural disturbances. Forest elephants (Loxodonta cyclotis) cause forest clearings within the tropics. This study was conducted at mid-elevations (1100–1700 m a.s.l.) in Mount Cameroon National Park. We assessed the difference [...] Read more.

Most of the tropical rainforests are subject to both anthropogenic and natural disturbances. Forest elephants (Loxodonta cyclotis) cause forest clearings within the tropics. This study was conducted at mid-elevations (1100–1700 m a.s.l.) in Mount Cameroon National Park. We assessed the difference in the structure of bird communities in the forest and areas located nearby affected by elephant activities. We used the point-count method; 22 points were established within each habitat. The vegetation was visually estimated within a 50 m radius surrounding each counting point. In total, 1603 birds from 85 species were recorded. The vegetation cover from 3 to 5 m at points with elephant activity was significantly lower compared to points without elephant activity. Bird species richness was significantly higher around points in pasture compared to points in intact forest. Habitat type and the percentage of vegetation layer from 3 to 5 m significantly impacted the bird community structure. The points in the pasture were especially characterized by the increased abundance of some open habitat species (e.g., Chubb’s Cisticola chubbi). Few studies have documented the effects of elephant activity on other species, although the effects are widely stated as important drivers of habitat diversity in tropical forests. In conclusion, disturbance caused by elephants leads to increased bird community diversity due to the increased heterogeneity of the environment, which documents the high importance of elephants as ecosystem engineers. Full article

(This article belongs to the Special Issue Birds in Temperate and Tropical Forests)

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14 pages, 3728 KiB

Open AccessArticle

The Impact of Different Biotopes and Management Practices on the Burden of Parasites in Artificial Nests of Osmia spp. (Megachilidae) Bees

by Ivana Tlak Gajger, Ivana Laklija, Mirko Jurković, Anja Košćević, Showket Ahmad Dar and Marija Ševar

Diversity 2022, 14(3), 226; https://doi.org/10.3390/d14030226 - 19 Mar 2022

Cited by 2 | Viewed by 2977

Abstract

The decline in pollinator insect abundance and diversity is increasing on a global scale. Major threats are the byproducts of numerous negative environmental pressures acting individually or in combination. They vary throughout different geographical areas, affecting the solitary bees differently. One of the [...] Read more.

The decline in pollinator insect abundance and diversity is increasing on a global scale. Major threats are the byproducts of numerous negative environmental pressures acting individually or in combination. They vary throughout different geographical areas, affecting the solitary bees differently. One of the most important negative pressures are the many parasites, predators and pests representing a threat to the successful reproduction of solitary bees in artificial nests. Especially vulnerable are the managed Osmia spp. bee populations reared for commercialization and trade. The primary goals of our monitoring study were: (i) to examine the presence and the prevalence of brood parasites in the various types of bees’ nesting material and in semi-field rearing conditions using the nest section analyses; (ii) to determine the presence of Nosema spp. in samples of feces and homogenized bee abdomens using a multiplex PCR method; (iii) the evaluation of the survival success level and emergence mass of healthy bees at each of the four studied bee rearing locations separately, depending on different environments and on the implementation of different managing practices. We determined the presence and prevalence of nest destructor parasites and accompanying fauna. Their presence was positively correlated with bee rearing failures. The results of this study may be used as a baseline for further solitary bee nest parasites monitoring schemes. Full article

(This article belongs to the Special Issue 2021 Feature Papers by Diversity’s Editorial Board Members)

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7 pages, 1287 KiB

Open AccessArticle

A Proposal for the Lectotype Designation of Ishige foliacea (Phaeophyceae, Ishigeaceae) Using DNA Barcoding

by Eun-Young Lee, Soon Jeong Lee and Sang-Rae Lee

Diversity 2022, 14(3), 225; https://doi.org/10.3390/d14030225 - 19 Mar 2022

Cited by 1 | Viewed by 2098

Abstract

Three species of the genus Ishige (Phaeophyceae, Ishigeaceae) are known from Korea, Japan and Mexico; they include Ishige foliacea Okamura, I. okamurae Yendo and I. sinicola (Setchell and N.L. Gardner) Chihara. Two species, I. foliacea and I. okamurae, are present in the [...] Read more.

Three species of the genus Ishige (Phaeophyceae, Ishigeaceae) are known from Korea, Japan and Mexico; they include Ishige foliacea Okamura, I. okamurae Yendo and I. sinicola (Setchell and N.L. Gardner) Chihara. Two species, I. foliacea and I. okamurae, are present in the algal flora of Korea and Japan. The original description of I. okamurae defined two forms of branches, filiform and foliose, but later the foliose branch was recognized as a new species I. foliacea, which is epiphytic on I. okamurae but can also be free-living. The currently proposed lectotype for I. foliacea is based on a free-living form and does not reflect the intent of the original description of the species. In this study, we conducted the DNA barcoding for herbarium specimens to identify Ishige species. Additionally, the variation in cox3 sequences obtained from I. okamurae specimens with two morphological forms collected from waters around the Korean Peninsula was sufficient to separate two species, I. okamurae and its epiphyte I. foliacea. The epiphytic I. foliacea on the lectotype specimen of I. okamurae is designated as lectotype I. foliacea. Full article

(This article belongs to the Special Issue Comparative and Functional Genomics of Land Plants)

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28 pages, 70752 KiB

Open AccessEditor’s ChoiceArticle

Island–to–Island Vicariance, Founder–Events and within–Area Speciation: The Biogeographic History of the Antillattus Clade (Salticidae: Euophryini)

by Franklyn Cala-Riquelme, Patrick Wiencek, Eduardo Florez-Daza, Greta J. Binford and Ingi Agnarsson

Diversity 2022, 14(3), 224; https://doi.org/10.3390/d14030224 - 18 Mar 2022

Cited by 7 | Viewed by 4118

Abstract

The Caribbean Archipelago is a biodiversity hotspot that plays a key role in developing our understanding of how dispersal ability affects species formation. In island systems, species with intermediate dispersal abilities tend to exhibit greater diversity, as may be the case for many [...] Read more.

The Caribbean Archipelago is a biodiversity hotspot that plays a key role in developing our understanding of how dispersal ability affects species formation. In island systems, species with intermediate dispersal abilities tend to exhibit greater diversity, as may be the case for many of the salticid lineages of the insular Caribbean. Here, we use molecular phylogenetic analyses to infer patterns of relationships and biogeographic history of the Caribbean endemic Antillattus clade (Antillattus, Truncattus, and Petemethis). We test if the timing of origin of the Antillatus clade in the Greater Antilles is congruent with GAARlandia and infer patterns of diversification within the Antillattus clade among Cuba, Hispaniola, and Puerto Rico. Specifically, we evaluate the relative roles of dispersal over land connections, and overwater dispersal events in diversification within the Greater Antilles. Time tree analysis and model-based inference of ancestral ranges estimated the ancestor of the Antillattus clade to be c. 25 Mya, and the best model suggests dispersal via GAARlandia from northern South America to Hispaniola. Hispaniola seems to be the nucleus from which ancestral populations dispersed into Cuba and Puerto Rico via land connections prior to the opening of the Mona Passage and the Windward Passage. Divergences between taxa of the Antillattus clade from Cuban, Hispaniolan, and Puerto Rican populations appear to have originated by vicariance, founder-events and within-island speciation, while multiple dispersal events (founder-events) between Cuba and Hispaniola during the Middle Miocene and the Late Miocene best explain diversity patterns in the genera Antillattus and Truncattus. Full article

(This article belongs to the Special Issue Phylogenomic, Biogeographic, and Evolutionary Research Trends in Arachnology)

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13 pages, 1817 KiB

Open AccessArticle

Interspecific Competition and Vertical Niche Partitioning in Fiji’s Forest Birds

by Alivereti N. Naikatini, Gunnar Keppel, Gilianne Brodie and Sonia Kleindorfer

Diversity 2022, 14(3), 223; https://doi.org/10.3390/d14030223 - 18 Mar 2022

Cited by 8 | Viewed by 3976

Abstract

Charles Darwin proposed his ‘principle of divergence’ to account for changes in traits that could promote speciation and coexistence of diverse forms through occupation of different niches to reduce interspecific competition. We explore interspecific foraging behaviour overlap in Fiji’s forest birds, and address [...] Read more.

Charles Darwin proposed his ‘principle of divergence’ to account for changes in traits that could promote speciation and coexistence of diverse forms through occupation of different niches to reduce interspecific competition. We explore interspecific foraging behaviour overlap in Fiji’s forest birds, and address two main questions: (1) Is there vertical stratification of foraging behavior? and (2) Is there evidence of interspecific competition driving the differences in foraging behaviour? We explore these questions across three foraging guilds, nectarivores (three species), insectivores (two species), and omnivores (two species), and find vertical portioning of foraging in each group. To investigate the effect of interspecific competition, we compared foraging heights of the Orange-breasted Myzomela (Myzomela jugularis) honeyeater on Viti Levu Island (where it coexists with two other honeyeater species) and Leleuvia Island (no other honeyeater species). On the main island Viti Levu, we found evidence for vertical niche partitioning within each foraging guild. On Leleuvia, with the ‘one-species only foraging guild’, Orange-breasted Myzomela occupied broader vertical foraging niche than on Viti Levu with two other competitor honeyeater species. This result supports the idea that vertical foraging height can be shaped by interspecific competition. The findings of this study support Darwin’s principle of divergence in Fiji’s forest birds for every foraging guild measured and adds to our understanding of the significance of interspecific competition and niche divergence for patterns of ecological speciation on islands. Full article

(This article belongs to the Special Issue Birds in Temperate and Tropical Forests)

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14 pages, 5431 KiB

Open AccessFeature PaperArticle

Reproductive Ecology of Distylous Shoreside Polygonum criopolitanum Hance

by Ming-Lin Chen, Meng-Ying Qi, Bei-Bei Bai and Xue Han

Diversity 2022, 14(3), 222; https://doi.org/10.3390/d14030222 - 18 Mar 2022

Cited by 2 | Viewed by 2257

Abstract

In this study, distyly was clearly confirmed in Polygonum criopolitanum Hance, which exhibited strict self-incompatibility. Unlike other distylous species, style-morph ratios of P. criopolitanum often deviated obviously from 1:1, and many populations were solely composed of long or short stylous flowers; the 1:1 [...] Read more.

In this study, distyly was clearly confirmed in Polygonum criopolitanum Hance, which exhibited strict self-incompatibility. Unlike other distylous species, style-morph ratios of P. criopolitanum often deviated obviously from 1:1, and many populations were solely composed of long or short stylous flowers; the 1:1 style-morph ratio was occasionally found in very large populations. P. criopolitanum was dimorphic for intrinsic features such as style height and anther height and ancillary features such as pollen size and number. The L-morph flowers produced a significantly smaller and higher number of pollen grains than the S-morph flowers, and the stigma papillae of both morphs were not significantly different. We nearly found no seed sets in most wild populations and very low seed sets occasionally occurred in large populations, which was different from other species of Polygonaceae. Mating experiments showed that P. criopolitanum has a strict self-incompatibility system and clonal propagation was more common than sexual propagation, which was adaptive with the unisexual wild populations. Hygrocolous habitat, 20–60% soil water content, and height gap less than 4 m to the adjacent water were the main limiting factors for the distribution of P. criopolitanum. Full article

(This article belongs to the Special Issue Ecology, Evolution and Diversity of Plants)

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40 pages, 13781 KiB

Open AccessReview

Skeletal Transformations and the Origin of Baleen Whales (Mammalia, Cetacea, Mysticeti): A Study on Evolutionary Patterns

by Michelangelo Bisconti and Giorgio Carnevale

Diversity 2022, 14(3), 221; https://doi.org/10.3390/d14030221 - 18 Mar 2022

Cited by 5 | Viewed by 7043

Abstract

A review of the morphological patterns exhibited by all the main radiations of mysticete (baleen whale) cetaceans provided a broad assessment of the fundamental morphological transformations that occurred in the transition to the Mysticeti clade. Skull and postcranial characters were illustrated, described and [...] Read more.

A review of the morphological patterns exhibited by all the main radiations of mysticete (baleen whale) cetaceans provided a broad assessment of the fundamental morphological transformations that occurred in the transition to the Mysticeti clade. Skull and postcranial characters were illustrated, described and compared, and their distribution was mapped on a combined phylogeny in the search for morphological support for the principal mysticete clades (i.e., Mysticeti, Chaeomysticeti and Balaenomorpha). In particular, characters of the skull (rostrum, vertex, temporal fossa, tympanic bulla and dentary) and the postcranial appendicular skeleton (scapula, humerus, radius and ulna) were all involved at different degrees in the process of morphological transformations leading to the modern-day mysticetes. Apart from a few typical characteristics of the rostrum that were already present in the earliest-diverging mysticetes (presence of lateral process of the maxilla, presence of multiple dorsal infraorbital foramina, thin lateral border of maxilla and presence of mesorostral groove), most of the other anatomical districts were unaffected by the transition so the earliest mysticetes show a number of archaeocete characters in the tympanic bulla, dentary and skull roof. The analysis of the whole dataset supported the hypothesis that the origin and evolution of mysticetes constituted a step-wise process and that the bauplan of the modern-day mysticetes was fully assembled at the level of the common ancestor of all Balaenomorpha. Full article

(This article belongs to the Special Issue Evolution of Crown Cetacea)

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19 pages, 26657 KiB

Open AccessArticle

De Novo Metagenomic Analysis of Microbial Community Contributing in Lignocellulose Degradation in Humus Samples Harvested from Cuc Phuong Tropical Forest in Vietnam

by Thi-Thu-Hong Le, Thi-Binh Nguyen, Hong-Duong Nguyen, Hai-Dang Nguyen, Ngoc-Giang Le, Trong-Khoa Dao, Thi-Quy Nguyen, Thi-Huyen Do and Nam-Hai Truong

Diversity 2022, 14(3), 220; https://doi.org/10.3390/d14030220 - 17 Mar 2022

Cited by 8 | Viewed by 3353

Abstract

We aimed to investigate the microbial diversity, mine lignocellulose-degrading enzymes/proteins, and analyze the domain structures of the mined enzymes/proteins in humus samples collected from the Cuc Phuong National Park, Vietnam. Using a high-throughput Illumina sequencer, 52 Gbs of microbial DNA were assembled in [...] Read more.

We aimed to investigate the microbial diversity, mine lignocellulose-degrading enzymes/proteins, and analyze the domain structures of the mined enzymes/proteins in humus samples collected from the Cuc Phuong National Park, Vietnam. Using a high-throughput Illumina sequencer, 52 Gbs of microbial DNA were assembled in 2,611,883 contigs, from which 4,104,872 open reading frames (ORFs) were identified. Among the total microbiome analyzed, bacteria occupied 99.69%; the five ubiquitous bacterial phyla included Proteobacteria, Bacteroidetes, Actinobacteria, Firmicutes, and Acidobacteria, which accounted for 92.59%. Proteobacteria (75.68%), the most dominant, was 5.77 folds higher than the second abundant phylum Bacteroidetes (13.11%). Considering the enzymes/proteins involved in lignocellulose degradation, 22,226 ORFs were obtained from the annotation analysis using a KEGG database. The estimated ratio of Proteobacteria/Bacteroidetes was approximately 1:1 for pretreatment and hemicellulases groups and 2.4:1 for cellulases. Furthermore, analysis of domain structures revealed their diversity in lignocellulose-degrading enzymes. CE and PL were two main families in pretreatment; GH1 and GH3-FN3 were the highest domains in the cellulase group, whereas GH2 and GH43 represented the hemicellulase group. These results validate that natural tropical forest soil could be considered as an important source to explore bacteria and novel enzymes/proteins for the degradation of lignocellulose. Full article

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14 pages, 2272 KiB

Open AccessEditor’s ChoiceArticle

Gradients in the Diversity of Plants and Large Herbivores Revealed with DNA Barcoding in a Semi-Arid African Savanna

by Patrick T. Freeman, Robert O. Ang’ila, Duncan Kimuyu, Paul M. Musili, David Kenfack, Peter Lokeny Etelej, Molly Magid, Brian A. Gill and Tyler R. Kartzinel

Diversity 2022, 14(3), 219; https://doi.org/10.3390/d14030219 - 17 Mar 2022

Cited by 8 | Viewed by 4355

Abstract

Do hotspots of plant biodiversity translate into hotspots in the abundance and diversity of large mammalian herbivores? A common expectation in community ecology is that the diversity of plants and animals should be positively correlated in space, as with the latitudinal diversity gradient [...] Read more.

Do hotspots of plant biodiversity translate into hotspots in the abundance and diversity of large mammalian herbivores? A common expectation in community ecology is that the diversity of plants and animals should be positively correlated in space, as with the latitudinal diversity gradient and the geographic mosaic of biodiversity. Whether this pattern ‘scales down’ to landscape-level linkages between the diversity of plants or the activities of highly mobile megafauna has received less attention. We investigated spatial associations between plants and large herbivores by integrating data from a plant-DNA-barcode phylogeny, camera traps, and a comprehensive map of woody plants across the 1.2-km² Mpala Forest Global Earth Observatory (ForestGEO) plot, Kenya. Plant and large herbivore communities were strongly associated with an underlying soil gradient, but the richness of large herbivore species was negatively correlated with the richness of woody plants. Results suggest thickets and steep terrain create associational refuges for plants by deterring megaherbivores from browsing on otherwise palatable species. Recent work using dietary DNA metabarcoding has demonstrated that large herbivores often directly control populations of the plant species they prefer to eat, and our results reinforce the important role of megaherbivores in shaping vegetation across landscapes. Full article

(This article belongs to the Special Issue Plant DNA Barcodes, Community Ecology, and Species Interactions)

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2 pages, 175 KiB

Open AccessEditorial

The Ecological Role of Salamanders as Prey and Predators

by Sebastiano Salvidio

Diversity 2022, 14(3), 218; https://doi.org/10.3390/d14030218 - 16 Mar 2022

Viewed by 2908

Abstract

Salamanders comprise more than 700 living species, mainly found in the Northern hemisphere (i [...] Full article

(This article belongs to the Special Issue The Ecological Role of Salamanders as Predators and Prey)

14 pages, 1026 KiB

Open AccessReview

Mechanisms Generating Dichotomies in the Life Strategies of Heterotrophic Marine Prokaryotes

by Tron Frede Thingstad, Lise Øvreås and Olav Vadstein

Diversity 2022, 14(3), 217; https://doi.org/10.3390/d14030217 - 16 Mar 2022

Cited by 5 | Viewed by 3141

Abstract

Understanding the mechanisms that generate and maintain diversity in marine prokaryotic communities is one of the main challenges for contemporary marine microbiology. We here review how observational, experimental, and theoretical evidence converge on the conclusion that the marine pelagic community of heterotrophic prokaryotes [...] Read more.

Understanding the mechanisms that generate and maintain diversity in marine prokaryotic communities is one of the main challenges for contemporary marine microbiology. We here review how observational, experimental, and theoretical evidence converge on the conclusion that the marine pelagic community of heterotrophic prokaryotes consists of organisms with two main types of life strategies. We illustrate this dichotomy by SAR11 and Vibrio spp. as typical representatives of the two strategies. A theory for life strategy dichotomy exists in classical r/K-selection. We here discuss an additional dichotomy introduced by what we term S/L-selection (for Small and Large, respectively). While r/K-selection focuses on the role of environmental disturbances, steady-state models suggest that high abundance at species level should be closely related to a low trade-off between competition and defense. We summarize literature indicating that the high availability of organic C is an essential environmental factor favoring Vibrio spp. and suggest that the essence of the generalized L-strategy is to reduce the competition-predator defense trade-off by using non-limiting organic C to increase size. The “streamlining” theory that has been suggested for the S-strategist SAR11 proposes the opposite: that low trade-off is achieved by a reduction in size. We show how this apparent contradiction disappears when the basic assumptions of diffusion-limited uptake are considered. We propose a classification scheme that combines S/L and r/K-selection using the two dimensions of organic C availability and environmental disturbance. As organic C in terrestrial runoff and size of the oligotrophic oceanic gyres are both changing, habitat size for both S- and L-strategists are affected by global change. A theory capturing the main aspects of prokaryote life strategies is therefore crucial for predicting responses of the marine microbial food web to climate change and other anthropogenic influences. Full article

(This article belongs to the Special Issue Ecology of Microbes in Marine and Estuarine Ecosystems)

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13 pages, 2585 KiB

Open AccessArticle

Red-Backed Shrike Lanius collurio Whole-Genome Sequencing Reveals Population Genetic Admixture

by Liviu G. Pârâu, Erjia Wang and Michael Wink

Diversity 2022, 14(3), 216; https://doi.org/10.3390/d14030216 - 16 Mar 2022

Viewed by 3146

Abstract

The Red-backed Shrike (Lanius collurio) is a medium-sized, carnivorous passerine, occurring throughout the western Palearctic. As with numerous other bird species, its numbers are declining, mainly due to anthropogenic factors. Therefore, revealing the population structure and genetic diversity is paramount in [...] Read more.

The Red-backed Shrike (Lanius collurio) is a medium-sized, carnivorous passerine, occurring throughout the western Palearctic. As with numerous other bird species, its numbers are declining, mainly due to anthropogenic factors. Therefore, revealing the population structure and genetic diversity is paramount in ensuring the survival of the species. However, until present, only mitochondrial DNA has been targeted to reveal the genetic structure of the species. These studies suggested a panmictic population structure. In this study, we employed next-generation sequencing of 88 Red-backed Shrikes from 11 countries and used single nucleotide polymorphisms (SNPs)) to investigate the population structure. Even with such high-resolution DNA data, we found considerable genetic variability, but our results indicate no genetic structure in the Red-backed Shrike, suggesting a panmictic population. Migrant birds from Israel and Kuwait could not be attributed to breeding populations. Panmixia is the genetic legacy of the widespread and continuous distribution of the species, high locomotion capacities, and, most importantly, the numerous ice ages from the past few million years, which forced various populations to retract to refugia and expand their ranges several times, and to interbreed both in the glacial refugia and during warm periods in Eurasia. Full article

(This article belongs to the Special Issue Diversity in 2022)

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21 pages, 8245 KiB

Open AccessEditor’s ChoiceArticle

Molecular Phylogenetics and Comparative Examination of Voucher Museums Reveal Two New Species of Gymnophthalmid Lizards (Squamata, Gymnophthalmidae) from the Peruvian Andes, with Comments on Proctoporus guentheri (Boettger, 1891)

by Luis Mamani, Roxana Cruz, Sergio Mallqui and Alessandro Catenazzi

Diversity 2022, 14(3), 215; https://doi.org/10.3390/d14030215 - 14 Mar 2022

Cited by 6 | Viewed by 5614

Abstract

The genus Proctoporus comprises cursorial and semifossorial lizards that inhabit the Andes of Argentina, Bolivia, and Peru. The taxonomy is complex, and many undescribed species and geographic gaps remain to be addressed. In this study, we use molecular phylogenetics and examine voucher museums [...] Read more.

The genus Proctoporus comprises cursorial and semifossorial lizards that inhabit the Andes of Argentina, Bolivia, and Peru. The taxonomy is complex, and many undescribed species and geographic gaps remain to be addressed. In this study, we use molecular phylogenetics and examine voucher museums to describe two new species of gymnophthalmid lizards from the montane forests of Cusco, on the eastern slopes of the Andes of Peru. We inferred phylogenetic relationships from concatenated sequences of four mitochondrial (12S, 16S, ND4, and Cytb) and one nuclear (c-mos) gene fragments, using a Maximum Likelihood approach and Bayesian Inference. We also examined and compared meristic traits of the specimens deposited in herpetological collections in Peru and Bolivia. Our molecular phylogeny had strong support for the monophyly of the subfamily Cercosaurinae, low support for the genus Proctoporus, and revealed two new taxa of Proctoporus. The two new species, which we name P. katerynae sp. nov. and P. optimus sp. nov., are characterized as having two rows of pregular scales and three anterior infralabials. Furthermore, we re-identified specimens assigned to P. laudahnae as P. guentheri, and we comment on the taxonomy of P. guentheri. Finally, we discuss how global climate change and human-caused habitat loss may threaten P. katerynae sp. nov. and P. optimus sp. nov. by the mechanism known as “Escalator to extinction”. Full article

(This article belongs to the Section Animal Diversity)

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16 pages, 1173 KiB

Open AccessArticle

Do Mixed Pinus yunnanensis Plantations Improve Soil’s Physicochemical Properties and Enzyme Activities?

by Chen Liang, Ling Liu, Zhixiao Zhang, Sangzi Ze, Mei Ji, Zongbo Li, Jinde Yu, Bin Yang and Ning Zhao

Diversity 2022, 14(3), 214; https://doi.org/10.3390/d14030214 - 14 Mar 2022

Cited by 5 | Viewed by 2481

Abstract

Many survival and ecological problems have emerged in Pinus yunnanensis pure pine forest plantations that are usually assumed to be solved by creating mixed plantations. On this basis, we determined the physicochemical properties and enzyme activities of three soil layers in pure and [...] Read more.

Many survival and ecological problems have emerged in Pinus yunnanensis pure pine forest plantations that are usually assumed to be solved by creating mixed plantations. On this basis, we determined the physicochemical properties and enzyme activities of three soil layers in pure and three types of mixed P. yunnanensis plantation stands (admixed species: Alnus nepalensis, Celtis tetrandra, and Quercus acutissima) in Southwest China. We used one-way ANOVA with Tukey’s test to analyze the effects of plantation type and depth on the soil’s properties and variations among different depths. Principal component analysis combined with cluster analysis was used to evaluate the soil quality of different forest types comprehensively. The results showed that the stand with a mixing proportion of 2:1 of P. yunnanensis and A. nepalensis, C. tetrandra, and Q. acutissima had higher total porosity, moisture content, total nitrogen, available phosphorus, total phosphorus, sucrase, urease, and catalase enzyme activities than other proportions of mixed forest and P. yunnanensis pine pure forest. In general, the mixed P. yunnanensis plantation could improve the soil quality, especially its chemical properties and enzymes. This study provides a basis for creating a mixed-mode of P. yunnanensis and other tree species that can not only improve the economy of forest land but also enhance the ecological value. Full article

(This article belongs to the Special Issue Mountain Biodiversity, Ecosystem Functioning and Services)

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23 pages, 1052 KiB

Open AccessEditor’s ChoiceReview

The Expanding Role of DNA Barcodes: Indispensable Tools for Ecology, Evolution, and Conservation

by Morgan R. Gostel and W. John Kress

Diversity 2022, 14(3), 213; https://doi.org/10.3390/d14030213 - 13 Mar 2022

Cited by 60 | Viewed by 13253

Abstract

DNA barcoding has transformed the fields of ecology, evolution, and conservation by providing a rapid and effective tool for species identification. The growth of DNA barcodes as a resource for biologists has followed advances in computational and sequencing technology that have enabled high-throughput [...] Read more.

DNA barcoding has transformed the fields of ecology, evolution, and conservation by providing a rapid and effective tool for species identification. The growth of DNA barcodes as a resource for biologists has followed advances in computational and sequencing technology that have enabled high-throughput barcoding applications. The global DNA barcode database is expanding to represent the diversity of species on Earth thanks to efforts by international consortia and expanding biological collections. Today, DNA barcoding is instrumental in advancing our understanding of how species evolve, how they interact, and how we can slow down their extirpation and extinction. This review focuses on current applications of DNA barcode sequences to address fundamental lines of research, as well as new and expanding applications of which DNA barcoding will play a central role. Full article

(This article belongs to the Special Issue Plant DNA Barcodes, Community Ecology, and Species Interactions)

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9 pages, 1147 KiB

Open AccessArticle

Applicability of Common Algorithms in Species–Area Relationship Model Fitting

by Zhidong Liu, Xiaoke Liu and Tsung-Jen Shen

Diversity 2022, 14(3), 212; https://doi.org/10.3390/d14030212 - 12 Mar 2022

Viewed by 2466

Abstract

The species–area relationship (SAR) describes a law of species richness changes as the sampling area varies. SAR has been studied for more than 100 years and is of great significance in the fields of biogeography, population ecology, and conservation biology. Accordingly, there are [...] Read more.

The species–area relationship (SAR) describes a law of species richness changes as the sampling area varies. SAR has been studied for more than 100 years and is of great significance in the fields of biogeography, population ecology, and conservation biology. Accordingly, there are many algorithms available for fitting the SARs, but their applicability is not numerically evaluated yet. Here, we have selected three widely used algorithms, and discuss three aspects of their applicability: the number of iterations, the time consumption, and the sensitivity to the initial parameter setting. Our results showed that, the Gauss–Newton method and the Levenberg–Marquardt method require relatively few iterative steps and take less time. In contrast, the Nelder–Mead method requires relatively more iteration steps and consumes the most time. Regarding the sensitivity of the algorithm to the initial parameters, the Gauss–Newton and the Nelder–Mead methods are more sensitive to the choice of initial parameters, while the Levenberg–Marquardt method is relatively insensitive to the choice of initial parameters. Considering that the Gauss–Newton method and the Levenberg–Marquardt method can only be used to fit smooth SAR models, we concluded that the Levenberg–Marquardt model is the best choice to fit the smooth SARs, while the Nelder–Mead method is the best choice to fit the non-smooth SARs. Full article

(This article belongs to the Special Issue Quantifying Biodiversity: Methods and Applications)

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17 pages, 739 KiB

Open AccessReview

Diversity and Biosynthetic Activities of Agarwood Associated Fungi

by Tian-Ye Du, Cheng-Jiao Dao, Ausana Mapook, Steven L. Stephenson, Abdallah M. Elgorban, Salim Al-Rejaie, Nakarin Suwannarach, Samantha C. Karunarathna and Saowaluck Tibpromma

Diversity 2022, 14(3), 211; https://doi.org/10.3390/d14030211 - 11 Mar 2022

Cited by 18 | Viewed by 4571

Abstract

Agarwood is a fragrant dark resin produced in plants belonging to the family Thyme-laeaceae and which has a high economic value. The unique fragrance and medicinal applications intensify the value of agarwood. The wild populations of agarwood trees are highly threatened by high [...] Read more.

Agarwood is a fragrant dark resin produced in plants belonging to the family Thyme-laeaceae and which has a high economic value. The unique fragrance and medicinal applications intensify the value of agarwood. The wild populations of agarwood trees are highly threatened by high economic demand. Therefore, it is worthwhile to develop an artificial agarwood induction technology for the countries that rely on agarwood from the natural habitat of the plants. Fungal induction of agarwood has been shown to be an efficient method. Interestingly, most of the fungi known from agarwood are endophytic. In this paper, we supplement and update the bioactivity of fungi associated with agarwood and their ability to induce agarwood formation. According to the existing literature, 59 endophytic fungal strains of 16 genera induce agarwood production, most of which belong to Fusarium (28 identified strains). Hence, Fusarium is a good candidate for further studies on fungal induced agarwood production. Full article

(This article belongs to the Topic Fungal Diversity)

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12 pages, 6642 KiB

Open AccessCommunication

Microsatellite Genotyping of Two Bulgarian Sheep Breeds

by Tsonka Odjakova, Pavel Todorov, Georgi Radoslavov and Peter Hristov

Diversity 2022, 14(3), 210; https://doi.org/10.3390/d14030210 - 11 Mar 2022

Cited by 6 | Viewed by 3134

Abstract

The aim of this study was to compare the genetic structure and genetic diversity of two Bulgarian sheep breeds. A total of 41 individuals from a modern Bulgarian sheep population (Rhodopean Tsigai, RT) and 46 representatives of a local Bulgarian sheep population (Middle [...] Read more.

The aim of this study was to compare the genetic structure and genetic diversity of two Bulgarian sheep breeds. A total of 41 individuals from a modern Bulgarian sheep population (Rhodopean Tsigai, RT) and 46 representatives of a local Bulgarian sheep population (Middle Rhodopean Sheep, MRS) were investigated based on 12 STR (short tandem repeat, also known as microsatellite) markers. In total, 121 alleles were found in the two populations using 12 microsatellite loci. The mean number of alleles, the effective number of alleles, and the polymorphism information content (PIC) values per loci were 10.08, 4.96, and 0.73, respectively. When comparing the allelic diversity across the populations, the highest Na was observed in the MRS breed (10.58 ± 0.87), while the value of this parameter in the RT breed was 9.58 ± 0.71. The largest genetic diversity was found at locus INRA005 with 14.5 alleles and the smallest polymorphism was noted for locus ETH152 with 5.5 alleles. The level of observed heterozygosity was in the range of 0.60 to 0.860. The expected heterozygosity level range was 0.62 to 0.87. When 12 microsatellite loci were compared, the INRA005 locus showed the highest level of genetic variability. Using Nei’s standard genetic distance, the observed genetic distance between the RT and MRS breeds was 0.103. Both sheep breeds demonstrated mixed genetic profiles based on the studied microsatellite markers. The clustering obtained by STRUCTURE analysis showed that the MRS breed is a more homogenous population, whereas the RT breed is more heterogenous. Full article

(This article belongs to the Special Issue Biodiversity Research in Bulgaria)

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17 pages, 4262 KiB

Open AccessArticle

Plant Species Turnover on Forest Gaps after Natural Disturbances in the Dinaric Fir Beech Forests (Omphalodo-Fagetum sylvaticae)

by Blanka Ravnjak, Jože Bavcon and Andraž Čarni

Diversity 2022, 14(3), 209; https://doi.org/10.3390/d14030209 - 11 Mar 2022

Cited by 6 | Viewed by 2696

Abstract

We studied species turnover and changes of ecological conditions and plant strategies on forest gaps created by natural disturbances (sleet, windthrow). We studied five forest gaps and a control plot within in the Dinaric silver fir-beech forest in the southern part of Slovenia. [...] Read more.

We studied species turnover and changes of ecological conditions and plant strategies on forest gaps created by natural disturbances (sleet, windthrow). We studied five forest gaps and a control plot within in the Dinaric silver fir-beech forest in the southern part of Slovenia. Forest gaps varied in age and size. The total number of recorded species in gaps was 184, with the highest number (106) at the largest forest gap and with the 58 species at the control locality in a juvenile beech forest. Forest gaps were predominantly colonised mostly by species of understory, forest margins, and forest clearings. The species presented in all forest gaps are representatives of the understory of beech forests. Species colonising forest gaps prefer habitats with more sunlight, medium wet to dry soil, and are tolerant to high daily and seasonal temperature fluctuations. In gaps, the community of plant species has a competitive strategy, which is also complemented with a stress-tolerator strategy. We determined that a forest gap represents a significant habitat patch, especially for those plant species which were not present there before. Full article

(This article belongs to the Special Issue Forest Management and Biodiversity Conservation)

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21 pages, 26163 KiB

Open AccessArticle

Effects of Landscape and Local Factors on the Diversity of Flower-Visitor Groups under an Urbanization Gradient, a Case Study in Wuhan, China

by Mengyu He, Nan Ran, Huiqian Jiang, Zemin Han, Yuanyong Dian, Xiaoxia Li, Dong Xie, Peter A. Bowler and Hui Wang

Diversity 2022, 14(3), 208; https://doi.org/10.3390/d14030208 - 11 Mar 2022

Cited by 8 | Viewed by 3525

Abstract

Urbanization is one of the primary forces driving worldwide pollinator decline. Moderate urban expansion with appropriate green space planning can help in maintaining pollinator diversity and pollination service. We investigated the relative effects of landscape and local factors on the diversity of flower-visitor [...] Read more.

Urbanization is one of the primary forces driving worldwide pollinator decline. Moderate urban expansion with appropriate green space planning can help in maintaining pollinator diversity and pollination service. We investigated the relative effects of landscape and local factors on the diversity of flower-visitor functional groups in a moderately urbanized city, Wuhan, located in central China. We found that the proportion of impervious surface had no significant effect on the number of visitations, but it was negatively associated with the diversity of flower-visitor groups. The number of visitations by Halictidae and Lepidoptera correlated positively with local flower density and flowering plant species richness, respectively. Flowering plant species richness was also positively correlated with the diversity of flower-visitor groups. The proportion of green space was negatively associated with the visitation number of Muscidae and the overall diversity of flower-visitor groups, revealing the potential influence of green space quality on pollinator assemblage. The pollination networks under three urbanization levels (with a total of 11 flower visitor groups and 43 plant species) were asymmetric, highly nested, and generalized. The suburb sites contained the highest diversity of interactions. Core flowering plants (Oenothera speciosa, Coreopsis grandiflora and Cyanus segetum) are exotic species with attractive flowers. Improving green space quality (high flower density and flowering plant species richness) and using attractive native flowering plants (Nandina domestica, Rosa chinensis, Astragalus sinicus, Cirsium arvense var. integrifolium, and Zabelia biflora) would enhance the function of urban green space to maintain pollinator diversity and ecosystem stability. Full article

(This article belongs to the Special Issue Ecology, Evolution and Diversity of Plants)

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17 pages, 1845 KiB

Open AccessArticle

Yeast and Lactic Acid Bacteria Dominate the Core Microbiome of Fermented ‘Hairy’ Tofu (Mao Tofu)

by Gian Maria Niccolò Benucci, Xinxin Wang, Li Zhang, Gregory Bonito and Fuqiang Yu

Diversity 2022, 14(3), 207; https://doi.org/10.3390/d14030207 - 11 Mar 2022

Cited by 7 | Viewed by 6101

Abstract

The process of fermenting tofu extends back thousands of years and is an indispensable part of Chinese culture. Despite a cultural resurgence in fermented foods and interest in microbiomes, there is little knowledge on the microbial diversity represented in fermented ‘hairy’ tofu, known [...] Read more.

The process of fermenting tofu extends back thousands of years and is an indispensable part of Chinese culture. Despite a cultural resurgence in fermented foods and interest in microbiomes, there is little knowledge on the microbial diversity represented in fermented ‘hairy’ tofu, known locally in China as Mao tofu. High-throughput metagenomic sequencing of the ITS, LSU and 16S rDNA was used to determine Mao tofu’s fungal and bacterial community diversity across four wet markets in Yunnan, China. The results show that hairy tofu in this region consists of around 170 fungal and 365 bacterial taxa, and that microbial taxa differ between markets. Diversity also differed based on the specific niche of the tofu block, comparing the outside rind-like niche to that of the inside of the tofu block. Machine learning random forest models were able to accurately classify both the market and niche of sample origin. An over-abundance of yeast and Geotrichum was found, and Mucor (Mucoromycota) was abundant in the outside rind-like niche, which consists of the visible ‘hairy’ mycelium. The majority of the bacterial OTUs belonged to Proteobacteria, Firmicutes, and Bacteroidetes, with Acinetobacter, Lactobacillus, Sphingobacterium and Flavobacterium the most abundant genera. Putative fungal pathogens of plants (Cercospora, Diaporthe, Fusarium) and animals (Metarhizium, Entomomortierella, Pyxidiophora, Candida, Clavispora) were also detected, as were putative bacterial pathogens identified as Legionella. Non-fungal eukaryotic taxa detected by LSU amplicon sequencing included soybean (Glycine max), Protozoa, Metazoa (e.g., Nematoda and Platyhelminthes), Rhizaria and Chromista, indicating that additional biodiversity exists in the hairy tofu microbiome. Full article

(This article belongs to the Special Issue The Hidden Fungal Diversity in Asia)

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11 pages, 980 KiB

Open AccessReview

Unraveling Techniques for Plant Microbiome Structure Analysis

by Supajit Sraphet and Bagher Javadi

Diversity 2022, 14(3), 206; https://doi.org/10.3390/d14030206 - 11 Mar 2022

Cited by 5 | Viewed by 3117

Abstract

Microbiome plays vital role in the life. Study the microbiome of plants with great impact in the planet can provide significant information to solve many problems. Therefore, finding structural population of plant microbiome needs scientific approach. Revealing the specific biochemical and genetical approaches [...] Read more.

Microbiome plays vital role in the life. Study the microbiome of plants with great impact in the planet can provide significant information to solve many problems. Therefore, finding structural population of plant microbiome needs scientific approach. Revealing the specific biochemical and genetical approaches towards identification of specific population provided the growing bodies of methods and procedures to study and analysis the plant microbiomes. Thus, this mini-review paper presents the summarized of scientific methods for study, identify and structural population analysis of plant microbiome. Full article

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14 pages, 19190 KiB

Open AccessArticle

Detection of the Endangered Stone Crayfish Austropotamobius torrentium (Schrank, 1803) and Its Congeneric A. pallipes in Its Last Italian Biotope by eDNA Analysis

by Chiara Manfrin, Massimo Zanetti, David Stanković, Umberto Fattori, Victoria Bertucci-Maresca, Piero G. Giulianini and Alberto Pallavicini

Diversity 2022, 14(3), 205; https://doi.org/10.3390/d14030205 - 10 Mar 2022

Cited by 7 | Viewed by 3756

Abstract

The stone crayfish, Austropotamobius torrentium, is a European freshwater crayfish. Although this species is relatively widespread throughout the continent, it is undergoing significant declines throughout its range. However, as the decline rates have not been quantified in detail, this species is classified [...] Read more.

The stone crayfish, Austropotamobius torrentium, is a European freshwater crayfish. Although this species is relatively widespread throughout the continent, it is undergoing significant declines throughout its range. However, as the decline rates have not been quantified in detail, this species is classified as data deficient by the IUCN Red List of Threatened Species. The present study describes the development and validation of two species-specific assays based on hydrolysis probe chemistry for the detection of A. torrentium and A. pallipes environmental DNA (eDNA) in water samples collected in the Julian Alps of Italy (Friuli Venezia Giulia). The eDNA-based method was applied to 14 sites within the Danubian Slizza basin, known to be inhabited by A. torrentium, but with insufficient information on their distribution. In addition, one station in the Tagliamento River basin was sampled to test the performance of the A. pallipes probe. The presence of A. torrentium is confirmed at 6 out of 15 sites. At four of these sites, A. torrentium is detected for the first time. In contrast, the presence of A. torrentium was not detected at two sites already known to harbour the species. Finally, the presence of A. pallipes was confirmed in the station belonging to the Tagliamento basin. The methodology described, which allows the distinction between the two species, paves the way for the parallel detection of the stone crayfish and the white-clawed crayfish (A. pallipes) through eDNA analysis. Full article

(This article belongs to the Special Issue eDNA for Basic and Applied Sciences)

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19 pages, 4161 KiB

Open AccessArticle

New Records of Powdery Mildews from Taiwan: Erysiphe ipomoeae comb. nov., E. aff. betae on Buckwheat, and E. neolycopersici comb. nov. on Cardiospermum halicacabum

by Hui-Yu Hsiao, Hiran A. Ariyawansa, Ching-Ching Hsu, Chao-Jen Wang and Yuan-Min Shen

Diversity 2022, 14(3), 204; https://doi.org/10.3390/d14030204 - 10 Mar 2022

Cited by 13 | Viewed by 4880

Abstract

Erysiphe is the largest genus of powdery mildews (PMs), a group of obligate plant pathogenic fungi. Exploration of biodiversity generally relies on regional surveys and our aim is to investigate the PMs in Taiwan. Collections of the fungi on five plant species around [...] Read more.

Erysiphe is the largest genus of powdery mildews (PMs), a group of obligate plant pathogenic fungi. Exploration of biodiversity generally relies on regional surveys and our aim is to investigate the PMs in Taiwan. Collections of the fungi on five plant species around agricultural environments were subjected to morphological and molecular characterization, using both internal transcribed spacer (ITS) and β-tubulin gene (TUB2) regions for the phylogenetic analyses. Erysipheipomoeae comb. nov., a species able to infect Ipomoea obscura and I. aquatica demonstrated by pathogenicity tests, has been neotypified. The two buckwheat species, Fagopyrum esculentum and F. tataricum, are found to be hosts of E. aff. betae. These results suggest that hosts in some plant families can be infected by more than one Erysiphe pathogen, e.g., Convolvulaceae by E. ipomoeae and E. convolvuli and Polygonaceae by E. polygoni and E. aff. betae, respectively. In addition, phylogenetic analyses of PMs on Cardiospermum halicacabum and tomato belonging to the E. aquilegiae complex are allocated under E. neolycopersici comb. nov. This extends the potential host range of E. aquilegiae complex to the plant family Sapindaceae. We conclude that awareness of the host associations of PMs can potentially benefit crop disease management. Full article

(This article belongs to the Special Issue The Hidden Fungal Diversity in Asia)

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14 pages, 2568 KiB

Open AccessArticle

DNA Barcoding and New Records of Odonates (Insecta: Odonata) from Paraíba State, Brazil

by Ricardo Koroiva, Vanessa Gabrielle Nóbrega Gomes and Diogo Silva Vilela

Diversity 2022, 14(3), 203; https://doi.org/10.3390/d14030203 - 10 Mar 2022

Cited by 5 | Viewed by 3900

Abstract

Odonates (Insecta: Odonata) are important insects in the food chains of freshwater environments around the world, being used as a model species for areas of behavior and analysis of environmental quality. In Brazil, especially in the Northeastern region, both knowledge about the distribution [...] Read more.

Odonates (Insecta: Odonata) are important insects in the food chains of freshwater environments around the world, being used as a model species for areas of behavior and analysis of environmental quality. In Brazil, especially in the Northeastern region, both knowledge about the distribution and molecular information of odonate species found in the two main biomes of the region is still limited. Aiming to improve these issues, here, we carried out an Odonata survey in two locations and built a DNA barcode database for species from the state of Paraíba. In total, 15 first records were reported for this Brazilian state and 142 specimens from 27 genera and 45 species had their ‘Folmer’ cytochrome c oxidase subunit I (COI) fragment evaluated. The database we generated includes data for 70% of the Odonata species found in Paraíba state. For 16 species, this is the first DNA barcode available in public sequence repositories. Our results demonstrate that using the COI in the regional scale can help identify and delimit those evaluated. Eight species (17%) showed a low percentage of differentiation (<2%) compared to other species currently deposited in the GenBank or BOLD System; nevertheless, we present morphological traits that reaffirm our identifications. Barcode data provide new insights into Neotropical diversity and deliver basic information for taxonomic analyses. Full article

(This article belongs to the Special Issue Diversity, Ecology and Evolution of Odonata)

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21 pages, 4136 KiB

Open AccessArticle

Response of Diatoms to the Changing Water Quality in the Myristica Swamps of the Western Ghats, India

by Mital Thacker and Balasubramanian Karthick

Diversity 2022, 14(3), 202; https://doi.org/10.3390/d14030202 - 9 Mar 2022

Cited by 9 | Viewed by 4771

Abstract

Myristica swamps are one of the rarest wetland ecosystems within the sub-tropical evergreen forests of the Western Ghats, India. As their name indicates, they harbor trees belonging to the ancient family Myristicaceae. Due to the waterlogged conditions and high humic decomposition, these [...] Read more.

Myristica swamps are one of the rarest wetland ecosystems within the sub-tropical evergreen forests of the Western Ghats, India. As their name indicates, they harbor trees belonging to the ancient family Myristicaceae. Due to the waterlogged conditions and high humic decomposition, these swamps are acidic, harbor rare and endemic biotas, and provide ecosystem services to humans. Monitoring this rare ecosystem is crucial because the swamps that once formed a large hydrological network across the Western Ghats are now confined to isolated patches due to human disturbance such as agricultural interventions, roads, and dam construction. Due to the change in land use, there is also a drastic change in water chemistry and associated biodiversity. Biomonitoring is more precise than physical and chemical monitoring. So, the current study aimed to undertake a comprehensive analysis of the physical, chemical, and biological assessment of these swamps. The diatom assemblages are strongly affected by water chemistry and serve as a powerful indicator of environmental changes in the freshwater aquatic systems. However, there is no information on diatom assemblages in these swamps, and the present study aimed to determine the diatom assemblage structure in the Myristica swamps and their response to changing water quality. Diatom samples were taken at 17 different swamps across the central Western Ghats, and a set of environmental parameters was evaluated. Analysis revealed a total of 91 species of diatoms belonging to 27 genera across the 17 sites, from which 44 diatom species showed restricted distribution to this unique environment. Overall, the dominant diatom genera inside the swamps included, Navicula (19.8%), Gomphonema (16%), Eunotia (13.3%), Ulnaria (9.4%), Achnanthidium (8%), Frustulia (6.2%), Planothidium (5.2%), and Brachysira (2.8%). High diatom species richness was observed in the swamps having less anthropogenic disturbance, and diatom assemblage composition was primarily determined by dissolved oxygen, pH, and conductivity. The significant number of geographically restricted taxa in this study points towards our limited understanding of this tropical biome and calls for a dire need for more studies from here, not only to improve our knowledge concerning the diversity, ecology, and biogeography of these diatoms but to further encourage their use in applied (paleo) environmental sciences. Our results indicate that diatoms can prove useful environmental indicators even in harsh environments like swamps and can be a potential tool for assessing ecological and climatic change. Full article

(This article belongs to the Special Issue Freshwater Siliceous Microeukaryotes)

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