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Life
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Microbial Composition and Function in Soil and Groundwater Systems
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Microbial Composition and Function in Soil and Groundwater Systems

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Microbiology".

Deadline for manuscript submissions: closed (20 November 2022) | Viewed by 12454

Special Issue Editors

Prof. Dr. Yizhi Sheng

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Guest Editor
State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China
Interests: microbial biogeochemistry; microbe-mineral interaction; soil and groundwater contamination; microbial ecology; hydrogeochemistry
Special Issues, Collections and Topics in MDPI journals
Dr. Juejie Yang

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Guest Editor
School of Grassland Science, Beijing Forestry University, Beijing 100083, China
Interests: soil ecology; microbial ecology; environmental science and related fields; biogeochemical cycle of carbon and nitrogen in grassland soil; microbial diversity and functional change; grassland ecosystem health evaluation; sustainable utilization of grassland resources.
Special Issues, Collections and Topics in MDPI journals
Dr. Liang Guo

E-Mail Website
Guest Editor
College of Geology and Environment, Xi’an University of Science and Technology, Xi’an 710054, China
Interests: groundwater microbiology; hydrochemistry; microbial diversity and function; biogeochemical cycle
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Over a century of research on microorganisms in natural environments has shed light on their diverse community compositions and versatile functions, allowing us to understand some of their critical roles in soil and groundwater systems. Diverse microbial communities are present in soil at numbers of approximately 108 to 109 cells per gram, while they are less diverse in groundwater systems due to the nutrient-depleted conditions. Their presence maintains the fertility of the soil, transforms nutrients, weathers minerals, affects groundwater chemistry, and degrades organic matter, generating labile materials useful to other organisms. Most activities and functions of microbial communities in soil and groundwater are the direct result of their astounding metabolic versatility, relying on chemoheterotrophic/chemolithotrophic reactions involving organic/inorganic compounds for sources of energy and nutrients. These activities and functions link the biosphere, lithosphere, hydrosphere, and atmosphere in the Earth’s critical zone. Aside from natural processes, anthropogenic activities transport contaminants across surface soil to vadose-zone soil and groundwater, causing both positive and negative feedback from microbial communities. The abilities of microbial communities to destroy or detoxify organic and inorganic contaminants (e.g., heavy metals) are of huge significance to environmental protection and human health. This Special Issue will therefore present advances in understanding the metabolism, distribution, and underlying drivers of microbial communities and their functions in both pristine and contaminated soil and groundwater systems, with the aim of improving our understanding of global nutrient biogeochemical cycles, contaminant bioremediation, biotechnology development, and the exploration of biological resources.

Dr. Yizhi Sheng
Dr. Juejie Yang
Dr. Liang Guo
Guest Editors

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Keywords

  • soil and groundwater
  • microbial community composition
  • element biogeochemical cycle
  • bioremediation
  • ecological restoration

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Published Papers (5 papers)

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Research

16 pages, 1161 KiB  
Article
Genetic Basis of Acinetobacter sp. K1 Adaptation Mechanisms to Extreme Environmental Conditions
by Nikola Petrová, Jana Kisková, Mariana Kolesárová and Peter Pristaš
Life 2023, 13(8), 1728; https://doi.org/10.3390/life13081728 - 11 Aug 2023
Cited by 2 | Viewed by 1429
Abstract
Anthropogenic pollution often leads to the generation of technosols, technogenic soils with inhospitable conditions for all living organisms including microbiota. Aluminum production near Ziar nad Hronom (Slovakia) resulted in the creation of a highly alkaline and heavy-metal-rich brown mud landfill, from which a [...] Read more.
Anthropogenic pollution often leads to the generation of technosols, technogenic soils with inhospitable conditions for all living organisms including microbiota. Aluminum production near Ziar nad Hronom (Slovakia) resulted in the creation of a highly alkaline and heavy-metal-rich brown mud landfill, from which a bacterial strain of a likely new species of the genus Acinetobacter, Acinetobacter sp. K1, was isolated. The whole-genome sequence analysis of this strain confirmed the presence of operon units enabling tolerance to the heavy metals copper, zinc, cobalt, cadmium, chromium, and metalloid arsenic, which are functionally active. Despite the predominance of plasmid-related sequences in the K1 genome, the results indicate that most of the resistance genes are chromosomally encoded. No significant alkali tolerance of Acinetobacter sp. K1 was observed in vitro, suggesting that community level mechanisms are responsible for the survival of this strain in the highly alkaline, brown mud bacterial community. Full article
(This article belongs to the Special Issue Microbial Composition and Function in Soil and Groundwater Systems)
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19 pages, 2257 KiB  
Article
Non-Aerated Common Nettle (Urtica dioica L.) Extract Enhances Green Beans (Phaseolus vulgaris L.) Growth and Soil Enzyme Activity
by Branka Maričić, Mia Brkljača, Dean Ban, Igor Palčić, Kristijan Franin, Šime Marcelić and Smiljana Goreta Ban
Life 2022, 12(12), 2145; https://doi.org/10.3390/life12122145 - 19 Dec 2022
Cited by 5 | Viewed by 2361
Abstract
One of the limiting factors in organic farming is the scarcity of allowed fertilizers and chemicals for plant protection. Plant and compost extracts are a promising solution for fertilization because of their positive effect on plant growth and soil microbial activity. Nettle extract [...] Read more.
One of the limiting factors in organic farming is the scarcity of allowed fertilizers and chemicals for plant protection. Plant and compost extracts are a promising solution for fertilization because of their positive effect on plant growth and soil microbial activity. Nettle extract was already successfully applied to some vegetables. Not-aerated nettle extract, obtained from dry nettle leaves, was applied in experiments with green beans in a quantity of 1 L per pot at two-day intervals was studied. A three-factorial experimental design was applied with two soil types (brown—Calcic Gleysol and red—Eutric Cambisol), soil disinfection with dazomet or not, and irrigated with nettle extract or water. Nettle extract application increased all above-ground traits; plant height, leaf area, flower buds, shoot dry weight at flowering, pod length, pod diameter, and shoot dry weight at harvest by 49%, 66%, 43%, 36%, 11%, 9%, and 37%, respectively, the root length at harvest by 59%, total yield by 48%, soil respiration by 91% and 74% in two soil types, and alkaline phosphatase by 30%. Dehydrogenase activity was enhanced by nettle extract application on red soil, while nettle extract application had no effect on root nodulation. The nettle extract application benefits in green bean organic production were attributed to the nutrients and other components present in the extract and not to nitrogen fixation. The optimization of the dose of the extract and experiments in real conditions of green bean production would be the next step toward the implementation of nettle extract as an organic fertilizer. Full article
(This article belongs to the Special Issue Microbial Composition and Function in Soil and Groundwater Systems)
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10 pages, 1674 KiB  
Article
Meta-Analysis of the Effect of Saline-Alkali Land Improvement and Utilization on Soil Organic Carbon
by Shuai Yang, Xinghai Hao, Yiming Xu, Juejie Yang and Derong Su
Life 2022, 12(11), 1870; https://doi.org/10.3390/life12111870 - 13 Nov 2022
Cited by 6 | Viewed by 3383
Abstract
There is a large amount of saline-alkali land in China. Through the improvement and utilization of saline-alkali land to improve the carbon content in soil, it can not only become a reserve resource of cultivated land or grazing grassland, but also become an [...] Read more.
There is a large amount of saline-alkali land in China. Through the improvement and utilization of saline-alkali land to improve the carbon content in soil, it can not only become a reserve resource of cultivated land or grazing grassland, but also become an important land “carbon sink”. In this study, we performed a comprehensive meta-analysis to identify the impact of improvement and utilization of saline-alkali soil on soil organic carbon (SOC) in China. Our results showed that the soil salt and alkali content in Heilongjiang Province and Jilin Province in China was the highest, with an SOC content between 3.05 and 17.8 g/kg and pH between 8.84 and 9.94. Among the five methods of reclamation, halophyte planting, fertilization, biochar and modifier application, only biochar and modifier application significantly increased the SOC content (p < 0.05). The content of SOC in saline-alkali soil was 2.9–6.3 g/kg before biochar application, and significantly increased to 6.2–13.05 g/kg after biochar application (p < 0.01). The SOC content was 3.05–8.12 g/kg before the application of the modifier, and significantly increased to 3.68–9 g/kg (p < 0.05) after the application of the modifier. After utilization and improvement of saline-alkali land, the total nitrogen, available phosphorus and available potassium also increased significantly (p < 0.05). This study provides a scientific basis for further understanding the improvement and utilization of saline-alkali land in China and its potential for increasing carbon sinks. Full article
(This article belongs to the Special Issue Microbial Composition and Function in Soil and Groundwater Systems)
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13 pages, 9590 KiB  
Article
Spatial Heterogeneity of Soil Bacterial Community Structure and Enzyme Activity along an Altitude Gradient in the Fanjingshan Area, Northeastern Guizhou Province, China
by Yuangui Xie, Lanyue Zhang, Juncai Wang, Meng Chen, Jiming Liu, Shengyang Xiao, Xiu Tian and Tingting Wu
Life 2022, 12(11), 1862; https://doi.org/10.3390/life12111862 - 12 Nov 2022
Cited by 4 | Viewed by 1644
Abstract
Changes in altitude can cause regional microclimate changes, leading to the spatial heterogeneity of environmental factors and soil bacteria. However, the internal driving process and mechanism remain unclear. Here, we selected Fanjingshan, a typical nature reserve in the subtropical region of south China [...] Read more.
Changes in altitude can cause regional microclimate changes, leading to the spatial heterogeneity of environmental factors and soil bacteria. However, the internal driving process and mechanism remain unclear. Here, we selected Fanjingshan, a typical nature reserve in the subtropical region of south China with a clear altitudinal belt, to reveal the response mechanisms of microbial populations with altitude changes. We examined the physiochemical and biological properties (pH and soil enzyme activities) of 0~10 cm soil layers, soil bacterial diversity, and community structure across the 2.1 km belt (consisting of six altitude ranges). Our results showed that soil pH was highest at the altitude range below 900 m and decreased with altitude thereafter. Soil enzyme activities showed an overall decreasing trend with altitude rising. The soil sucrase and catalase activity was highest (48.35 mg.g−1.d−1 and 23.75 µmol.g−1, respectively) at altitudes below 900 m; the soil urease activity was highest (704.24 µg.g−1.d−1) at 900~1200 m; and the soil acid phosphatase activity was highest (57.18 µmol.g−1) at 1200~1500 m. In addition, the soil bacterial community diversity showed a linear increasing trend, with the maximum abundance at 1500~1800 m. Soil pH was correlated with enzyme activity and bacterial community composition and structure, and the correlation was the strongest between pH and the distribution of bacterial diversity at altitudes below 900 m. Overall, soil enzyme activities and soil bacterial diversity showed spatial heterogeneity along the altitude gradient, and their community structure and composition were affected by altitude as a result of changes in soil physicochemical factors. This study provides a better and deeper understanding of the spatial succession of soil in the Fanjingshan area and the distribution pattern of soil microorganisms in central subtropical mountain ecosystems. Full article
(This article belongs to the Special Issue Microbial Composition and Function in Soil and Groundwater Systems)
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14 pages, 788 KiB  
Article
Bacterial Communities Associated with Crude Oil Bioremediation through Composting Approaches with Indigenous Bacterial Isolate
by Nilita Mukjang, Thararat Chitov, Wuttichai Mhuantong, Verawat Champreda, Wasu Pathom-aree, Pachara Sattayawat and Sakunnee Bovonsombut
Life 2022, 12(11), 1712; https://doi.org/10.3390/life12111712 - 27 Oct 2022
Cited by 7 | Viewed by 2268
Abstract
In this study, we aim to investigate the efficiency of crude oil bioremediation through composting and culture-assisted composting. First, forty-eight bacteria were isolated from a crude oil-contaminated soil, and the isolate with the highest crude oil degradation activity, identified as Pseudomonas aeruginosa, [...] Read more.
In this study, we aim to investigate the efficiency of crude oil bioremediation through composting and culture-assisted composting. First, forty-eight bacteria were isolated from a crude oil-contaminated soil, and the isolate with the highest crude oil degradation activity, identified as Pseudomonas aeruginosa, was selected. The bioremediation was then investigated and compared between crude oil-contaminated soil (S), the contaminated soil composted with fruit-based waste (SW), and the contaminated soil composted with the same waste with the addition of the selected bacterium (SWB). Both compost-based methods showed high efficiencies of crude oil bioremediation (78.1% and 83.84% for SW and SWB, respectively). However, only a slight difference between the treatments without and with the addition of P. aeruginosa was observed. To make a clear understanding of this point, bacterial communities throughout the 4-week bioremediation period were analyzed. It was found that the community dynamics between both composted treatments were similar, which corresponds with their similar bioremediation efficiencies. Interestingly, Pseudomonas disappeared from the system after one week, which suggests that this genus was not the key degrader or only involved in the early stage of the process. Altogether, our results elaborate that fruit-based composting is an effective approach for crude oil bioremediation. Full article
(This article belongs to the Special Issue Microbial Composition and Function in Soil and Groundwater Systems)
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