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Forests
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Forest Microbial Communities and Processes
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Forest Microbial Communities and Processes

A special issue of Forests (ISSN 1999-4907). This special issue belongs to the section "Forest Ecology and Management".

Deadline for manuscript submissions: closed (5 November 2019) | Viewed by 29464

Special Issue Editor

Prof. Dr. Robert Bradley

E-Mail Website
Guest Editor
Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada
Interests: soil biodiversity; plant-soil interactions; ecological succession; agroforestry; greenhouse gases; carbon and nitrogen cycling; soil biology and biochemistry

Special Issue Information

Dear Colleagues,

Microbial communities are the unseen biomass largely responsible for the functioning of forest ecosystems. Their activities control important processes such as litter decomposition, nutrient cycling, plant diversity, nitrogen fixation, and plant nutrient uptake. They play key ecological roles wherever they may occur, whether it be in the bulk soil, in the rhizosphere, on leaf surfaces, within symbiotic structures, or as plant endophytes. In order to highlight the many contributions of microbes to the functioning of forest ecosystems, we are inviting the submission of manuscripts presenting original research results on (1) the factors controlling the structure and distribution of forest microbial populations or communities, or (2) key forest ecological processes (e.g., N2 fixation, decomposition, nutrient cycling, etc.) that are regulated by microbes.

Please note that this special issue will not publish studies that are wholly descriptive, such as those that characterize microbial communities in various forest environments. Rather, such information should be used in further experiments to test an idea or a mechanism, or to formulate novel conclusions.

Prof. Dr. Robert Bradley
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Forests is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • forest ecosystem functions
  • microbial communities
  • community structure and distribution
  • nutrient cycling
  • plant–soil interactions

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Published Papers (7 papers)

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Research

18 pages, 3788 KiB  
Article
Boreal Forest Multifunctionality Is Promoted by Low Soil Organic Matter Content and High Regional Bacterial Biodiversity in Northeastern Canada
by Roxanne Giguère-Tremblay, Genevieve Laperriere, Arthur de Grandpré, Amélie Morneault, Danny Bisson, Pierre-Luc Chagnon, Hugo Germain and Vincent Maire
Forests 2020, 11(2), 149; https://doi.org/10.3390/f11020149 - 29 Jan 2020
Cited by 11 | Viewed by 3497
Abstract
Boreal forests provide important ecosystem services, most notably being the mitigation of increasing atmospheric CO2 emissions. Microbial biodiversity, particularly the local diversity of fungi, has been shown to promote multiple functions of the boreal forests of Northeastern China. However, this microbial biodiversity-multifunctionality [...] Read more.
Boreal forests provide important ecosystem services, most notably being the mitigation of increasing atmospheric CO2 emissions. Microbial biodiversity, particularly the local diversity of fungi, has been shown to promote multiple functions of the boreal forests of Northeastern China. However, this microbial biodiversity-multifunctionality relationship has yet to be explored in Northeastern Canada, where historical environment have shaped a different regional pool of microbial diversity. This study focuses on the relationship between the soil microbiome and ecosystem multifunctionality, as well as the influence of pH and redox potential (Eh) on the regulation of such relationship. Structural equation modelling (SEM) was used to explore the different causal relationships existing in the studied ecosystems. In a managed part of the Canadian boreal forest, 156 forest polygons were sampled to (1) estimate the α- and β-diversity of fungal and bacterial communities and (2) measure 12 ecosystem functions mainly related to soil nutrient storage and cycling. Both bacteria and fungi influenced ecosystem multifunctionality, but on their own respective functions. Bacterial β-diversity was the most important factor increasing primary productivity and soil microbial biomass, while reducing soil emitted atmospheric CO2. Environmental characteristics, particularly low levels of organic matter in soil, were shown to have the strongest positive impact on boreal ecosystem multifunctionality. Overall, our results were consistent with those obtained in Northeastern China; however, some differences need to be further explored especially considering the history of forest management in Northeastern Canada. Full article
(This article belongs to the Special Issue Forest Microbial Communities and Processes)
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20 pages, 4262 KiB  
Article
Estimation of Fungal Diversity and Identification of Major Abiotic Drivers Influencing Fungal Richness and Communities in Northern Temperate and Boreal Quebec Forests
by Laperriere Genevieve, Chagnon Pierre-Luc, Giguère-Tremblay Roxanne, Morneault Amélie, Bisson Danny, Maire Vincent and Germain Hugo
Forests 2019, 10(12), 1096; https://doi.org/10.3390/f10121096 - 2 Dec 2019
Cited by 18 | Viewed by 3933
Abstract
Fungi play important roles in forest ecosystems and understanding fungal diversity is crucial to address essential questions about species conservation and ecosystems management. Changes in fungal diversity can have severe impacts on ecosystem functionality. Unfortunately, little is known about fungal diversity in northern [...] Read more.
Fungi play important roles in forest ecosystems and understanding fungal diversity is crucial to address essential questions about species conservation and ecosystems management. Changes in fungal diversity can have severe impacts on ecosystem functionality. Unfortunately, little is known about fungal diversity in northern temperate and boreal forests, and we have yet to understand how abiotic variables shape fungal richness and composition. Our objectives were to make an overview of the fungal richness and the community composition in the region and identify their major abiotic drivers. We sampled 262 stands across the northern temperate and boreal Quebec forest located in the region of Abitibi-Témiscamingue, Mauricie, and Haute-Mauricie. At each site, we characterized fungal composition using Illumina sequencing, as well as several potential abiotic drivers (e.g., humus thickness, soil pH, vegetation cover, etc.). We tested effects of abiotic drivers on species richness using generalized linear models, while difference in fungal composition between stands was analyzed with permutational multivariate analysis of variance and beta-diversity partitioning analyses. Fungi from the order Agaricales, Helotiales, and Russulales were the most frequent and sites from the north of Abitibi-Témiscamingue showed the highest OTUs (Operational Taxonomic Unit) richness. Stand age and moss cover were the best predictors of fungal richness. On the other hand, the strongest drivers of fungal community structure were soil pH, average cumulative precipitation, and stand age, although much of community variance was left unexplained in our models. Overall, our regional metacommunity was characterized by high turnover rate, even when rare OTUs were removed. This may indicate strong environmental filtering by several unmeasured abiotic filters, or stronger than expected dispersal limitations in soil fungal communities. Our results show how difficult it can be to predict fungal community assembly even with high replication and efforts to include several biologically relevant explanatory variables. Full article
(This article belongs to the Special Issue Forest Microbial Communities and Processes)
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18 pages, 2261 KiB  
Article
The Contrasting Responses of Mycorrhizal Fungal Mycelium Associated with Woody Plants to Multiple Environmental Factors
by Cunguo Wang, Shengwei Zong and Mai-He Li
Forests 2019, 10(11), 973; https://doi.org/10.3390/f10110973 - 4 Nov 2019
Cited by 5 | Viewed by 3224
Abstract
Research Highlights: Extraradical mycorrhizal fungal mycelium (MFM) plays critical roles in nutrient absorption and carbon cycling in forest ecosystems. However, it is often ignored or treated as a root uptake apparatus in existing biogeochemical models. Methods: We conducted a meta-analysis to reveal how [...] Read more.
Research Highlights: Extraradical mycorrhizal fungal mycelium (MFM) plays critical roles in nutrient absorption and carbon cycling in forest ecosystems. However, it is often ignored or treated as a root uptake apparatus in existing biogeochemical models. Methods: We conducted a meta-analysis to reveal how MFM responds to various, coinciding environmental factors and their interactions. Results: Nitrogen (N) addition and N-phosphorus (P)-potassium (K) combination significantly decreased MFM. However, elevated CO2, organic matter addition, P addition, and CO2-N combination significantly increased MFM. In contrast, warming, K addition, N-P combination, and P-K combination did not affect MFM. Mycorrhizal fungal levels (individual vs. community), mycorrhizal type (ectomycorrhizal fungi vs. arbuscular mycorrhizal fungi), treatment time (<1 year vs. >1 year), and mycelium estimation/sampling method (biomarker vs. non-biomarker; ingrowth mesh bag vs. soil core) significantly affected the responses of MFM to elevated CO2 and N addition. The effect sizes of N addition significantly increased with mean annual precipitation, but decreased with soil pH and host tree age. The effect sizes of P addition significantly increased with N concentration in host plant leaves. Conclusions: The differential responses revealed emphasize the importance of incorporating MFM in existing biogeochemical models to precisely assess and predict the impacts of global changes on forest ecosystem functions. Full article
(This article belongs to the Special Issue Forest Microbial Communities and Processes)
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15 pages, 3101 KiB  
Article
Effects of Warming and Nitrogen Addition on the Soil Bacterial Community in a Subtropical Chinese Fir Plantation
by Lin Xie, Qunjie Zhang, Jiling Cao, Xiaofei Liu, Decheng Xiong, Qian Kong and Yusheng Yang
Forests 2019, 10(10), 861; https://doi.org/10.3390/f10100861 - 2 Oct 2019
Cited by 15 | Viewed by 3002
Abstract
Soil warming has the potential to alter bacterial communities, affecting carbon (C) storage and nitrogen (N) cycling in forest ecosystems. We studied bacterial community changes by warming soil and adding two N-levels (40 and 80 kg N ha−1 year−1) for [...] Read more.
Soil warming has the potential to alter bacterial communities, affecting carbon (C) storage and nitrogen (N) cycling in forest ecosystems. We studied bacterial community changes by warming soil and adding two N-levels (40 and 80 kg N ha−1 year−1) for two years in a subtropical plantation of Chinese fir (Cunninghamia lanceolate (Lamb.) Hook) in southern China. Soil warming significantly changed the bacterial community structure, causing decreases in Proteobacteria and Acidobacteria, while increasing Actinobacteria and Chloroflexi. The high N addition had a greater impact on the bacterial community structure than the low N addition. Warming shifted the bacterial community towards oligotrophic taxa, while N addition could dilute this tendency. Results of the ecological networks indicated that warming resulted in a more complicated co-occurrence network and an increased interaction between different phylum communities, while N addition enhanced the cooperation within communities pertaining to the same phylum. The changes to the soil properties, typical catabolism enzymes, and plant growth also showed that soil warming and N addition accelerated the C and N cycles in the soil, and lead to an increased upward flow of N (from underground to aboveground) and decomposition rate of soil organic carbon (SOC). Overall, the results provided insights into the bacterial community and soil C and N cycling change at a subtropical plantation. Full article
(This article belongs to the Special Issue Forest Microbial Communities and Processes)
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14 pages, 1654 KiB  
Article
Arbuscular Mycorrhizal Fungi Associated with Tree Species in a Planted Forest of Eastern China
by Jinping Wang, G. Geoff Wang, Bo Zhang, Zhongming Yuan, Zhiyuan Fu, Yingdan Yuan, Lingjun Zhu, Shilin Ma and Jinchi Zhang
Forests 2019, 10(5), 424; https://doi.org/10.3390/f10050424 - 16 May 2019
Cited by 50 | Viewed by 5274
Abstract
Arbuscular mycorrhizal fungi (AMF) play an important role in the establishment and maintenance of plant communities in forest ecosystems. Most previous studies about AMF have been conducted in natural forests, and little attention has been paid to trees in planted forests. This study [...] Read more.
Arbuscular mycorrhizal fungi (AMF) play an important role in the establishment and maintenance of plant communities in forest ecosystems. Most previous studies about AMF have been conducted in natural forests, and little attention has been paid to trees in planted forests. This study investigated AMF associated with tree species and the relationships between edaphic factors and AMF communities in a planted forest of eastern China. We found high total AMF colonization rates in the roots of Carya illinoensis (Wangenh.) K. Koch, Zelkova serrata (Thunb.) Makinoz, Taxodium ‘zhongshansha’, Eucommia ulmoides Oliv., and Elaeagnus pungens Thunb., ranging from 62.07% to 100%, indicating that AMF can establish effective symbiotic relationships with these tree species. The AMF colonization rate was significantly and negatively correlated with soil phosphorus, while AMF colonization intensity was significantly and negatively correlated with soil moisture content, total carbon, and organic matter content. Spore density was in the range of 4.38 to 76.38 spores per g soil. In total, 35 AMF species from 10 genera were identified. Glomus and Acaulospora were the dominant genera. Acaulospora foveata and Septoglomus constrictum were the dominant species. AMF communities differed among the tree species and were closely related to edaphic factors, and AMF diversity was significantly related to soil carbon and pH. Our results revealed the colonization, community, and diversity of AMF associated with tree species, as well as their relationships with edaphic factors, in planted forests. Our findings can be used to provide insight on the utilization and management of AMF to maintain sustainable management of planted forests. Full article
(This article belongs to the Special Issue Forest Microbial Communities and Processes)
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16 pages, 1744 KiB  
Article
The Effect of Forest Thinning on Soil Microbial Community Structure and Function
by Ran Wu, Xiaoqin Cheng and Hairong Han
Forests 2019, 10(4), 352; https://doi.org/10.3390/f10040352 - 23 Apr 2019
Cited by 34 | Viewed by 5522
Abstract
Microbial communities and their associated enzyme activities play key roles in carbon cycling in ecosystems. Forest thinning is likely to change the soil properties and feedbacks on the structure and function of microbial communities, consequently affecting microbial regulation on the soil carbon process. [...] Read more.
Microbial communities and their associated enzyme activities play key roles in carbon cycling in ecosystems. Forest thinning is likely to change the soil properties and feedbacks on the structure and function of microbial communities, consequently affecting microbial regulation on the soil carbon process. However, few studies have focused on the mechanism of how thinning affects the quantity and stability of soil carbon. To reveal the influence of thinning on soil carbon and to explore the regulated key factors, this study was conducted in a pure Larix principis-rupprechtii Mayr plantation with different thinning intensity (light, medium, and high) in Shanxi province, China. Soil properties (soil pH, soil water content, soil organic carbon, and soil microbial biomass carbon) were measured. Meanwhile, soil microbial communities were examined with the method of phospholipid fatty acid (PLFA), and soil enzyme activities were measured as indicators of soil microbial functions. The results showed that medium and high thinning has positive effects on soil organic carbon, microbial biomass carbon, soil microbial abundance, and soil enzyme activities. Actinomycetes and gram-negative bacteria were the major factors to affect soil microbial community function relating to carbon decomposition. Soil pH contributed to actinomycetes and gram-negative bacteria through direct influences on arbuscular mycorrhizal fungi. Moreover, there were strong correlations between soil pH and microbial community to control soil carbon turnover. The increasing of soil microbial abundance and the microbial regulation on soil carbon in forest thinning need to be considered for sustainable forest management practices in northern China. Full article
(This article belongs to the Special Issue Forest Microbial Communities and Processes)
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Graphical abstract

13 pages, 2119 KiB  
Article
Leaf-Associated Shifts in Bacterial and Fungal Communities in Response to Chicken Rearing Under Moso Bamboo Forests in Subtropical China
by Xiaoping Zhang, Zheke Zhong, Xu Gai, Jiafu Ying, Weifen Li, Xuhua Du, Fangyuan Bian and Chuanbao Yang
Forests 2019, 10(3), 216; https://doi.org/10.3390/f10030216 - 1 Mar 2019
Cited by 10 | Viewed by 3393
Abstract
Integrated bamboo-chicken farming (BCF) systems are a traditional agroforestry pattern with large economic benefits in subtropical China. However, little is known regarding the effect of this integration on the bamboo leaf-associated microbiome, which can be very important for disease control and nutrient turnover. [...] Read more.
Integrated bamboo-chicken farming (BCF) systems are a traditional agroforestry pattern with large economic benefits in subtropical China. However, little is known regarding the effect of this integration on the bamboo leaf-associated microbiome, which can be very important for disease control and nutrient turnover. In the present study, we compared the leaf-associated bacterial and fungal communities of moso bamboo (Phyllostachys edulis) in a BCF system and an adjacent moso bamboo forest (MBF). The results showed that Cyanobacteria and Ascomycota were the predominant microbial phyla associated with bamboo leaves. Chicken farming under the bamboo forest significantly increased the bacterial and fungal alpha diversity (observed operational taxonomic units (OTUs) and Simpson’s index) associated with bamboo leaves. Principal components analysis (PCoA) further confirmed the shifts in the bacterial and fungal communities caused by chicken farming. Based on the observed relative abundances, the phyla Bacteroidetes, Actinobacteria, TM7, and Basidiomycota were significantly increased on BCF-associated leaves compared with MBF leaves, while Acidobacteria and Ascomycota were significantly decreased. An ecological function prediction analysis based on metabolic processes indicated that BCF could accelerate nutrient (C, N, and S) cycling but may increase the risk of fungal-associated diseases. Our findings suggest that shifts in leaf-associated bacterial and fungal communities can be important indicators for the scientific management of BCF systems. Full article
(This article belongs to the Special Issue Forest Microbial Communities and Processes)
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