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Microorganisms
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Soil Microbial Diversity and Its Ecological Functions
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Soil Microbial Diversity and Its Ecological Functions

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Environmental Microbiology".

Deadline for manuscript submissions: closed (31 March 2023) | Viewed by 30479

Special Issue Editors

Prof. Dr. Huixin Li

E-Mail Website
Guest Editor
College of Resources and Environmental Sciences, Nanjing Agricultural University, Weigang, No. 1, Nanjing 210095, China
Interests: soil ecology; interaction between soil fauna and microbe
Prof. Dr. Li Xu

E-Mail Website
Guest Editor
College of Resources and Environmental Sciences, Nanjing Agricultural University, Weigang, No. 1, Nanjing 210095, Jiangsu, China
Interests: environmental microbiology; bioremediation; interaction between plant and microbe
Prof. Dr. Hui Cao

E-Mail Website
Guest Editor
College of Life Sciences, Nanjing Agricultural University, Weigang, No. 1, Nanjing 210095, Jiangsu, China
Interests: soil microbial diversity and ecological function; autotrophic bacteria and carbon fixation

Special Issue Information

Dear Colleagues,

Soils harbor highly diverse microbial communities that play an essential role in simultaneously maintaining multiple ecosystem functions that are critical for the nutrient biogeochemical cycle, soil-structure formation, primary production, litter decomposition, climate regulation, etc. The capacity of soils to sustain such functions is a key feature known as “soil health/quality”, and the soil microbiome is suggested as a potential indicator for assessing soil quality. In the past two decades, many studies have investigated the relationship between biodiversity and ecosystem function, most of which have focused on a limited set of ecosystem variables. Both anthropogenic and natural disturbances, such as land-use patterns, fertilizer/pesticide application and climate change, can severely impact multifunctionality in terrestrial ecosystems through manipulating the belowground soil microbial diversity and interactions. The introduction of new techniques in microbial ecology has led to many descriptive studies and surveys. The sequences of 16S/18S rRNA genes and functional genes tell us ‘who is there’, while metagenomic, metatranscriptomic and other omics-based approaches further describe what the organisms might be able to do or, less frequently, what they are doing. However, the knowledge and understanding of soil microbial ecology is still limited. For example, what are the factors that determine the microbial composition and community assembly in soils, how does the microbial community structure significantly influence ecosystem function, how and why do communities and their activities respond to environmental changes, and what are the interactions between soil microorganisms and fauna, especially in the rhizosphere? Therefore, effective and up-to-date research on soil’s microbial diversity and its ecological functions is urgently needed. This Special Issue of Microorganisms focuses on the current state of knowledge on soil microbial diversity, ecological function, community assembly and geographical distribution. All innovative research papers on soil microbial communities in different environments are welcome, and cutting-edge methods or technologies for exploring soil microbial ecology are also appropriate. Examples of topics that fit the scope of the Special Issue are as follows:

  1. The driving factors and assembly mechanisms of soil microbial communities under anthropogenic and natural disturbances, including, but not limited to, drying–wetting, freezing–thawing, heavy-metal, organic-pollutant, solid-waste, microplastic, and radioactive-contaminant conditions.
  2. The illustration of the relationship between the soil microbial community composition and ecosystem function under various terrestrial ecosystems, such as grassland, forest land and farmland.
  3. The geographical distribution patterns of soil microorganisms at local and global scales.
  4. The interactions between soil microorganisms and fauna, especially in the rhizosphere.
  5. Innovations in the theory and technology of assessments and potential solutions for soil microbial ecology.

Prof. Dr. Huixin Li
Prof. Dr. Li Xu
Prof. Dr. Hui Cao
Guest Editors

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. Microorganisms 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 2700 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

  • soil microbial community
  • soil degradation
  • soil pollution
  • ecological function
  • soil fauna
  • rhizosphere
  • food web
  • ecological network
  • microbial community assembly
  • environmental microbiology
  • agricultural microbiology
  • microbial biogeography

Published Papers (16 papers)

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Research

13 pages, 1649 KiB  
Article
The Application of Organic Matter Temporarily Shifts Carrot Prokaryotic Communities in the Endosphere but Not in the Rhizosphere
by Irem Bagci, Kazuki Suzuki, Rasit Asiloglu and Naoki Harada
Microorganisms 2023, 11(10), 2377; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms11102377 - 23 Sep 2023
Viewed by 804
Abstract
Endophytic prokaryotes, bacteria, and archaea, are important microorganisms that benefit host plants by promoting plant growth and reducing stress. The objective of this study was to evaluate temporal shifts in the root endophytic prokaryotic communities associated with carrots (Daucus carota subsp. sativus [...] Read more.
Endophytic prokaryotes, bacteria, and archaea, are important microorganisms that benefit host plants by promoting plant growth and reducing stress. The objective of this study was to evaluate temporal shifts in the root endophytic prokaryotic communities associated with carrots (Daucus carota subsp. sativus) and the effect of organic matter application on them. Carrots were grown in a planter under five fertilizer treatments (weed compost, bark compost, cattle manure, chemical fertilizer, and no-fertilizer control) and the compositions of rhizosphere and root endosphere prokaryotic communities were determined via amplicon sequencing analysis targeting the 16S rRNA gene at 60 and 108 days after sowing. The results showed that the rhizosphere prokaryotic community compositions were stable despite different sampling times and fertilizer treatments; however, a greater temporal shift and an effect of the type of organic matter applied were observed in the endosphere prokaryotic communities. The differences in treatments resulted in significant differences in the abundance and Faith pyrogenetic diversity of the endosphere prokaryotic community. Genera, such as Burkholderia, Sphingomonas, and Rhodanobacter, that exhibit plant-growth-promoting and biocontrol activities, were detected regardless of the treatments, suggesting that they may play an important ecological role as the core endophytes in carrot roots. Full article
(This article belongs to the Special Issue Soil Microbial Diversity and Its Ecological Functions)
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19 pages, 7032 KiB  
Article
Effect of Heavy-Metal-Resistant PGPR Inoculants on Growth, Rhizosphere Microbiome and Remediation Potential of Miscanthus × giganteus in Zinc-Contaminated Soil
by Anna Muratova, Sergey Golubev, Valeria Romanova, Irina Sungurtseva and Asil Nurzhanova
Microorganisms 2023, 11(6), 1516; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms11061516 - 07 Jun 2023
Cited by 4 | Viewed by 1561
Abstract
Microbial-assisted phytoremediation is considered a more effective approach to soil rehabilitation than the sole use of plants. Mycolicibacterium sp. Pb113 and Chitinophaga sp. Zn19, heavy-metal-resistant PGPR strains originally isolated from the rhizosphere of Miscanthus × giganteus, were used as inoculants of the [...] Read more.
Microbial-assisted phytoremediation is considered a more effective approach to soil rehabilitation than the sole use of plants. Mycolicibacterium sp. Pb113 and Chitinophaga sp. Zn19, heavy-metal-resistant PGPR strains originally isolated from the rhizosphere of Miscanthus × giganteus, were used as inoculants of the host plant grown in control and zinc-contaminated (1650 mg/kg) soil in a 4-month pot experiment. The diversity and taxonomic structure of the rhizosphere microbiomes, assessed with metagenomic analysis of rhizosphere samples for the 16S rRNA gene, were studied. Principal coordinate analysis showed differences in the formation of the microbiomes, which was affected by zinc rather than by the inoculants. Bacterial taxa affected by zinc and the inoculants, and the taxa potentially involved in the promotion of plant growth as well as in assisted phytoremediation, were identified. Both inoculants promoted miscanthus growth, but only Chitinophaga sp. Zn19 contributed to significant Zn accumulation in the aboveground part of the plant. In this study, the positive effect of miscanthus inoculation with Mycolicibacterium spp. and Chitinophaga spp. was demonstrated for the first time. On the basis of our data, the bacterial strains studied may be recommended to improve the efficiency of M. × giganteus phytoremediation of zinc-contaminated soil. Full article
(This article belongs to the Special Issue Soil Microbial Diversity and Its Ecological Functions)
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14 pages, 3783 KiB  
Article
Effects of Degradation on Microbial Communities of an Amazonian Mangrove
by Gleyciane Machado da Costa, Sávio Souza Costa, Rafael Azevedo Baraúna, Bruno Pureza Castilho, Izabel Cruz Pinheiro, Artur Silva, Ana Paula Schaan, Ândrea Ribeiro-dos-Santos and Diego Assis das Graças
Microorganisms 2023, 11(6), 1389; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms11061389 - 25 May 2023
Cited by 3 | Viewed by 1341
Abstract
Mangroves provide a unique ecological environment for complex microbial communities, which play important roles in biogeochemical cycles, such as those for carbon, sulfur, and nitrogen. Microbial diversity analyses of these ecosystems help us understand the changes caused by external influences. Amazonian mangroves occupy [...] Read more.
Mangroves provide a unique ecological environment for complex microbial communities, which play important roles in biogeochemical cycles, such as those for carbon, sulfur, and nitrogen. Microbial diversity analyses of these ecosystems help us understand the changes caused by external influences. Amazonian mangroves occupy an area of 9000 km2, corresponding to 70% of the mangroves in Brazil, on which studies of microbial biodiversity are extremely scarce. The present study aimed to determine changes in microbial community structure along the PA-458 highway, which fragmented a mangrove zone. Mangrove samples were collected from three zones, (i) degraded, (ii) in the process of recovery, and (iii) preserved. Total DNA was extracted and submitted for 16S rDNA amplification and sequencing on an MiSeq platform. Subsequently, reads were processed for quality control and biodiversity analyses. The most abundant phyla were Proteobacteria, Firmicutes, and Bacteroidetes in all three mangrove locations, but in significantly different proportions. We observed a considerable reduction in diversity in the degraded zone. Important genera involved in sulfur, carbon, and nitrogen metabolism were absent or dramatically reduced in this zone. Our results show that human impact in the mangrove areas, caused by the construction of the PA-458 highway, has resulted in a loss of biodiversity. Full article
(This article belongs to the Special Issue Soil Microbial Diversity and Its Ecological Functions)
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16 pages, 2515 KiB  
Article
Apple Root Microbiome as Indicator of Plant Adaptation to Apple Replant Diseased Soils
by Nivethika Ajeethan, Shawkat Ali, Keith D. Fuller, Lord Abbey and Svetlana N. Yurgel
Microorganisms 2023, 11(6), 1372; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms11061372 - 24 May 2023
Viewed by 1663
Abstract
The tree fruit industry in Nova Scotia, Canada, is dominated by the apple (Malus domestica) sector. However, the sector is faced with numerous challenges, including apple replant disease (ARD), which is a well-known problem in areas with intensive apple cultivation. A [...] Read more.
The tree fruit industry in Nova Scotia, Canada, is dominated by the apple (Malus domestica) sector. However, the sector is faced with numerous challenges, including apple replant disease (ARD), which is a well-known problem in areas with intensive apple cultivation. A study was performed using 16S rRNA/18S rRNA and 16S rRNA/ITS2 amplicon sequencing to assess soil- and root-associated microbiomes, respectively, from mature apple orchards and soil microbiomes alone from uncultivated soil. The results indicated significant (p < 0.05) differences in soil microbial community structure and composition between uncultivated soil and cultivated apple orchard soil. We identified an increase in the number of potential pathogens in the orchard soil compared to uncultivated soil. At the same time, we detected a significant (p < 0.05) increase in relative abundances of several potential plant-growth-promoting or biocontrol microorganisms and non-fungal eukaryotes capable of promoting the proliferation of bacterial biocontrol agents in orchard soils. Additionally, the apple roots accumulated several potential PGP bacteria from Proteobacteria and Actinobacteria phyla, while the relative abundances of fungal taxa with the potential to contribute to ARD, such as Nectriaceae and plant pathogenic Fusarium spp., were decreased in the apple root microbiome compared to the soil microbiome. The results suggest that the health of a mature apple tree can be ascribed to a complex interaction between potential pathogenic and plant growth-promoting microorganisms in the soil and on apple roots. Full article
(This article belongs to the Special Issue Soil Microbial Diversity and Its Ecological Functions)
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17 pages, 1527 KiB  
Article
Structure of Microbial Communities and Biological Activity in Tundra Soils of the Euro-Arctic Region (Rybachy Peninsula, Russia)
by Maria V. Korneykova, Vladimir A. Myazin, Nadezhda V. Fokina, Alexandra A. Chaporgina, Dmitry A. Nikitin and Andrey V. Dolgikh
Microorganisms 2023, 11(5), 1352; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms11051352 - 22 May 2023
Cited by 3 | Viewed by 1351
Abstract
The relevance of the Arctic regions’ study is rapidly increasing due to the sensitive response of fragile ecosystems to climate change and anthropogenic pressure. The microbiome is an important component that determines the soils’ functioning and an indicator of changes occurring in ecosystems. [...] Read more.
The relevance of the Arctic regions’ study is rapidly increasing due to the sensitive response of fragile ecosystems to climate change and anthropogenic pressure. The microbiome is an important component that determines the soils’ functioning and an indicator of changes occurring in ecosystems. Rybachy Peninsula is the northernmost part of the continental European Russia and is almost completely surrounded by Barents Sea water. For the first time, the microbial communities of the Entic Podzol, Albic Podzol, Rheic Histosol and Folic Histosol as well as anthropogenically disturbed soils (chemical pollution and human impact, growing crops) on the Rybachy Peninsula were characterized using plating and fluorescence microscopy methods, in parallel with the enzymatic activity of soils. The amount and structure of soil microbial biomass, such as the total biomass of fungi and prokaryote, the length and diameter of fungal and actinomycete mycelium, the proportion of spores and mycelium in the fungal biomass, the number of spores and prokaryotic cells, the proportion of small and large fungal spores and their morphology were determined. In the soils of the peninsula, the fungal biomass varied from 0.121 to 0.669 mg/g soil. The biomass of prokaryotes in soils ranged from 9.22 to 55.45 μg/g of soil. Fungi predominated, the proportion of which in the total microbial biomass varied from 78.5 to 97.7%. The number of culturable microfungi ranged from 0.53 to 13.93 × 103 CFU/g in the topsoil horizons, with a maximum in Entic Podzol and Albic Podzol soils and a minimum in anthropogenically disturbed soil. The number of culturable copiotrophic bacteria varied from 41.8 × 103 cells/g in a cryogenic spot to 5551.3 × 103 cells /g in anthropogenically disturbed soils. The number of culturable oligotrophic bacteria ranged from 77.9 to 12,059.6 × 103 cells/g. Changes in natural soils because of anthropogenic impact and a change in vegetation types have led to a change in the structure of the community of soil microorganisms. Investigated tundra soils had high enzymatic activity in native and anthropogenic conditions. The β-glucosidase and urease activity were comparable or even higher than in the soils of more southern natural zone, and the activity of dehydrogenase was 2–5 times lower. Thus, despite the subarctic climatic conditions, local soils have a significant biological activity upon which the productivity of ecosystems largely depends. The soils of the Rybachy Peninsula have a powerful enzyme pool due to the high adaptive potential of soil microorganisms to the extreme conditions of the Arctic, which allows them to perform their functions even under conditions of anthropogenic interference. Full article
(This article belongs to the Special Issue Soil Microbial Diversity and Its Ecological Functions)
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20 pages, 3046 KiB  
Article
The Application of Sulfur Influences Microbiome of Soybean Rhizosphere and Nutrient-Mobilizing Bacteria in Andosol
by Jean Louise Cocson Damo, Takashi Shimizu, Hinako Sugiura, Saki Yamamoto, Shin-ichiro Agake, Julieta Anarna, Haruo Tanaka, Soh Sugihara, Shin Okazaki, Tadashi Yokoyama, Michiko Yasuda and Naoko Ohkama-Ohtsu
Microorganisms 2023, 11(5), 1193; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms11051193 - 03 May 2023
Cited by 1 | Viewed by 1950
Abstract
This study aimed to determine the effect of sulfur (S) application on a root-associated microbial community resulting in a rhizosphere microbiome with better nutrient mobilizing capacity. Soybean plants were cultivated with or without S application, the organic acids secreted from the roots were [...] Read more.
This study aimed to determine the effect of sulfur (S) application on a root-associated microbial community resulting in a rhizosphere microbiome with better nutrient mobilizing capacity. Soybean plants were cultivated with or without S application, the organic acids secreted from the roots were compared. High-throughput sequencing of 16S rRNA was used to analyze the effect of S on microbial community structure of the soybean rhizosphere. Several plant growth-promoting bacteria (PGPB) isolated from the rhizosphere were identified that can be harnessed for crop productivity. The amount of malic acid secreted from the soybean roots was significantly induced by S application. According to the microbiota analysis, the relative abundance of Polaromonas, identified to have positive association with malic acid, and arylsulfatase-producing Pseudomonas, were increased in S-applied soil. Burkholderia sp. JSA5, obtained from S-applied soil, showed multiple nutrient-mobilizing traits among the isolates. In this study, S application affected the soybean rhizosphere bacterial community structure, suggesting the contribution of changing plant conditions such as in the increase in organic acid secretion. Not only the shift of the microbiota but also isolated strains from S-fertilized soil showed PGPB activity, as well as isolated bacteria that have the potential to be harnessed for crop productivity. Full article
(This article belongs to the Special Issue Soil Microbial Diversity and Its Ecological Functions)
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16 pages, 2751 KiB  
Article
Salinity Impacts the Functional mcrA and dsrA Gene Abundances in Everglades Marshes
by Deidra Jordan, John S. Kominoski, Shelby Servais and DeEtta Mills
Microorganisms 2023, 11(5), 1180; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms11051180 - 30 Apr 2023
Viewed by 1364
Abstract
Coastal wetlands, such as the Everglades, are increasingly being exposed to stressors that have the potential to modify their existing ecological processes because of global climate change. Their soil microbiomes include a population of organisms important for biogeochemical cycling, but continual stresses can [...] Read more.
Coastal wetlands, such as the Everglades, are increasingly being exposed to stressors that have the potential to modify their existing ecological processes because of global climate change. Their soil microbiomes include a population of organisms important for biogeochemical cycling, but continual stresses can disturb the community’s composition, causing functional changes. The Everglades feature wetlands with varied salinity levels, implying that they contain microbial communities with a variety of salt tolerances and microbial functions. Therefore, tracking the effects of stresses on these populations in freshwater and brackish marshes is critical. The study addressed this by utilizing next generation sequencing (NGS) to construct a baseline soil microbial community. The carbon and sulfur cycles were studied by sequencing a microbial functional gene involved in each process, the mcrA and dsrA functional genes, respectively. Saline was introduced over two years to observe the taxonomic alterations that occurred after a long-term disturbance such as seawater intrusion. It was observed that saltwater dosing increased sulfite reduction in freshwater peat soils and decreased methylotrophy in brackish peat soils. These findings add to the understanding of microbiomes by demonstrating how changes in soil qualities impact communities both before and after a disturbance such as saltwater intrusion. Full article
(This article belongs to the Special Issue Soil Microbial Diversity and Its Ecological Functions)
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18 pages, 3070 KiB  
Article
Divergent Changes in Bacterial Functionality as Affected by Root-Zone Ecological Restoration in an Aged Peach Orchard
by Na Sun, Weiwei Zhang, Shangqiang Liao and Hong Li
Microorganisms 2022, 10(11), 2127; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10112127 - 27 Oct 2022
Cited by 2 | Viewed by 1279
Abstract
Soil restoration is a crucial approach to improving plant productivity in orchards with soil degradation, yield reduction, and fruit quality declination in China. A self-invented root-zone ecological restoration practice (RERP) with soil conditioner, or organic fertilizer, was employed in a degraded peach orchard [...] Read more.
Soil restoration is a crucial approach to improving plant productivity in orchards with soil degradation, yield reduction, and fruit quality declination in China. A self-invented root-zone ecological restoration practice (RERP) with soil conditioner, or organic fertilizer, was employed in a degraded peach orchard in Beijing in 2020 to investigate the consequent impacts on soil bacterial composition and functionality at soil depths of 0–20 cm and 20–40 cm. Bacterial diversity was sensitive to RERP, especially in subsurface soil. RERP with soil conditioner significantly increased bacterial diversity, and affected abundances of certain genera, such as a significantly increased amount of Bacillus in surface soil and Blastococcus, Microvirga, Nocardioides, and Sphingomonas in subsurface soil. It also significantly affected abundances of bacterial functions related to metabolism in subsurface soil, particularly those with low abundance such as decreased transcription abundance and increased amino acid metabolism abundance. Soil bacterial functions were observably affected by bacterial diversity and composition, particularly in the deep soil layer. RERP affected bacterial functionality via responses of soil bacteria and bacteria-mediated alterations to the changed soil property. Correlation analysis between soil properties, bacterial taxonomy, and bacterial functions revealed that RERP affected bacterial functionality by altering the soil microenvironment with ample nutrients and water supply in root zone. Consequently, shifted bacterial functionality could have a potential in orchard ecosystem services in view of fruit yield and quality. Taken together, RERP had notably positive impacts on soil bacterial diversity and functions, and a prospect of increased plant productivity in the degrade orchard ecosystem. Full article
(This article belongs to the Special Issue Soil Microbial Diversity and Its Ecological Functions)
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15 pages, 1545 KiB  
Article
View from the Top: Insights into the Diversity and Community Assembly of Ectomycorrhizal and Saprotrophic Fungi along an Altitudinal Gradient in Chinese Boreal Larix gmelinii-Dominated Forests
by Yi Guo, Li Ji, Mingwei Wang, Chengfeng Shan, Fangyuan Shen, Yuchun Yang, Gongxiu He, Witoon Purahong and Lixue Yang
Microorganisms 2022, 10(10), 1997; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10101997 - 10 Oct 2022
Cited by 2 | Viewed by 1480
Abstract
The altitudinal patterns of soil fungi have attracted considerable attention; however, few studies have investigated the diversity and community assembly of fungal functional guilds along an altitudinal gradient. Here, we explored ectomycorrhizal (EcM) and saprotrophic (SAP) fungal diversity and community assembly along a [...] Read more.
The altitudinal patterns of soil fungi have attracted considerable attention; however, few studies have investigated the diversity and community assembly of fungal functional guilds along an altitudinal gradient. Here, we explored ectomycorrhizal (EcM) and saprotrophic (SAP) fungal diversity and community assembly along a 470 m vertical gradient (ranging from 830 to 1300 m) on Oakley Mountain, sampling bulk soils in the 0–10 cm and 10–20 cm soil layers of Larix gmelinii-dominated forests. Illumina MiSeq sequencing of the ITS genes was employed to explore the fungal community composition and diversity. The relative abundance of EcM and SAP fungi showed a divergent pattern along an altitudinal gradient, while we observed a consistent altitudinal tendency for EcM and SAP fungal diversity and community assembly. The diversity of both fungal guilds increased with increasing altitude. Altitude and soil moisture were the key factors affecting the community composition of both fungal guilds. In addition, the plant community composition significantly affected the EcM fungal community composition, whereas the dissolved organic nitrogen and ammonium nitrogen contents were the driving factors of SAP fungal community. Despite the effects of vegetation and soil factors, EcM and SAP fungal communities were mainly governed by stochastic processes (especially drift) at different altitudes and soil depths. These results shed new light on the ecology of different fungal functional guilds along an altitudinal gradient, which will provide a deeper understanding of the biogeography of soil fungi. Full article
(This article belongs to the Special Issue Soil Microbial Diversity and Its Ecological Functions)
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14 pages, 1965 KiB  
Article
The Effect of Microbial Diversity and Biomass on Microbial Respiration in Two Soils along the Soil Chronosequence
by Jakub Vicena, Masoud M. Ardestani, Petr Baldrian and Jan Frouz
Microorganisms 2022, 10(10), 1920; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10101920 - 27 Sep 2022
Cited by 7 | Viewed by 2011
Abstract
Microbial diversity plays an important role in the decomposition of soil organic matter. However, the pattern and drivers of the relationship between microbial diversity and decomposition remain unclear. In this study, we followed the decomposition of organic matter in soils where microbial diversity [...] Read more.
Microbial diversity plays an important role in the decomposition of soil organic matter. However, the pattern and drivers of the relationship between microbial diversity and decomposition remain unclear. In this study, we followed the decomposition of organic matter in soils where microbial diversity was experimentally manipulated. To produce a gradient of microbial diversity, we used soil samples at two sites of the same chronosequence after brown coal mining in Sokolov, Czech Republic. Soils were X-ray sterilized and inoculated by two densities of inoculum from both soils and planted with seeds of six local plant species. This created two soils each with four levels of microbial diversity characterized by next-generation sequencing. These eight soils were supplied, or not, by litter of the bushgrass Calamagrostis epigejos, and microbial respiration was measured to assess the rate of decomposition. A strong positive correlation was found between microbial diversity and decomposition of organic matter per gram of carbon in soil, which suggests that microbial diversity supports decomposition if the microbial community is limited by available carbon. In contrast, microbial respiration per gram of soil negatively correlated with bacterial diversity and positively with fungal biomass, suggesting that in the absence of a carbon limitation, decomposition rate is controlled by the amount of fungal biomass. Soils with the addition of grass litter showed a priming effect in the initial stage of decomposition compared to the samples without the addition of litter. Thus, the relationship between microbial diversity and the rate of decomposition may be complex and context dependent. Full article
(This article belongs to the Special Issue Soil Microbial Diversity and Its Ecological Functions)
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17 pages, 2829 KiB  
Article
Biogeographical Patterns and Assembly of Bacterial Communities in Saline Soils of Northeast China
by Xiaolong Liang, Xiaoyu Wang, Ning Zhang and Bingxue Li
Microorganisms 2022, 10(9), 1787; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10091787 - 05 Sep 2022
Cited by 5 | Viewed by 1865
Abstract
Increasing salinity undermines soil fertility and imposes great threats to soil ecosystem productivity and ecological sustainability. Microbes with the ability to adapt to environmental adversity have gained increasing attention for maintenance and restoration of the salt-affected soil ecosystem structure and functioning; however, the [...] Read more.
Increasing salinity undermines soil fertility and imposes great threats to soil ecosystem productivity and ecological sustainability. Microbes with the ability to adapt to environmental adversity have gained increasing attention for maintenance and restoration of the salt-affected soil ecosystem structure and functioning; however, the characterization of microbial communities in saline–sodic soils remains limited. This study characterized the bacterial community composition and diversity in saline–sodic soils along a latitude gradient across Northeast China, aiming to reveal the mechanism of physicochemical and geographic characteristics shaping the soil bacterial communities. Our results showed that the bacterial community composition and diversity were significantly impacted by soil pH, electrical conductivity, Na+, K+, Cl−, and CO32−. Significant differences in bacterial diversity were revealed along the latitude gradient, and the soil factors accounted for 58.58% of the total variations in bacterial community composition. Proteobacteria, Actinobacteria, Gemmatimonadetes, Chloroflexi, and Bacteroidetes were dominant across all samples. Actinobacteria and Gemmatimonadetes were significantly enriched in high soil sodicity and salinity, while Acidobacteria and Proteobacteria were suppressed by high pH and salt stress in the saline–sodic soils. Increase in soil pH and salinity significantly decreased bacterial species richness and diversity. Community composition analysis indicated that bacterial taxonomic groups (e.g., Bacillus, Egicoccus, Truepera, Halomonas, and Nitrolancea) that may adapt well to high salinity were greatly enriched in the examined soils. The findings collectively evidenced that bacterial community composition and diversity in a broad biographic scale were determined by niche-based environmental characteristics and biotic interactions. The profiling of the soil bacterial communities along the latitude gradient will also provide a basis for a better understanding of the salt-affected soil ecosystem functioning and restoration of these soil ecosystems. Full article
(This article belongs to the Special Issue Soil Microbial Diversity and Its Ecological Functions)
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21 pages, 2463 KiB  
Article
Soil pH, Calcium Content and Bacteria as Major Factors Responsible for the Distribution of the Known Fraction of the DNA Bacteriophage Populations in Soils of Luxembourg
by Perrine Florent, Henry-Michel Cauchie, Malte Herold, Stéphan Jacquet and Leslie Ogorzaly
Microorganisms 2022, 10(7), 1458; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10071458 - 19 Jul 2022
Cited by 5 | Viewed by 2610
Abstract
Bacteriophages participate in soil life by influencing bacterial community structure and function, biogeochemical cycling and horizontal gene transfer. Despite their great abundance, diversity, and importance in microbial processes, they remain little explored in environmental studies. The influence of abiotic factors on the persistence [...] Read more.
Bacteriophages participate in soil life by influencing bacterial community structure and function, biogeochemical cycling and horizontal gene transfer. Despite their great abundance, diversity, and importance in microbial processes, they remain little explored in environmental studies. The influence of abiotic factors on the persistence of bacteriophages is now recognized; however, it has been mainly studied under experimental conditions. This study aimed to determine whether the abiotic factors well-known to influence bacteriophage persistence also control the natural distribution of the known DNA bacteriophage populations. To this end, soil from eight study sites including forests and grasslands located in the Attert River basin (Grand Duchy of Luxembourg) were sampled, covering different soil and land cover characteristics. Shotgun metagenomics, reference-based bioinformatics and statistical analyses allowed characterising the diversity of known DNA bacteriophage and bacterial communities. After combining soil properties with the identified DNA bacteriophage populations, our in-situ study highlighted the influence of pH and calcium cations on the diversity of the known fraction of the soil DNA bacteriophages. More interestingly, significant relationships were established between bacteriophage and bacterial populations. This study provides new insights into the importance of abiotic and biotic factors in the distribution of DNA bacteriophages and the natural ecology of terrestrial bacteriophages. Full article
(This article belongs to the Special Issue Soil Microbial Diversity and Its Ecological Functions)
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13 pages, 2016 KiB  
Article
Composition, Structure and Diversity of Soil Bacterial Communities before, during and after Transit through the Gut of the Earthworm Aporrectodea caliginosa
by Manuel Aira, Marcos Pérez-Losada, Keith A. Crandall and Jorge Domínguez
Microorganisms 2022, 10(5), 1025; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10051025 - 13 May 2022
Cited by 12 | Viewed by 2438
Abstract
Earthworms heavily modify the soil microbiome as it passes throughout their guts. However, there are no detailed studies describing changes in the composition, structure and diversity of soil microbiomes during gut transit and once they are released back to the soil as casts. [...] Read more.
Earthworms heavily modify the soil microbiome as it passes throughout their guts. However, there are no detailed studies describing changes in the composition, structure and diversity of soil microbiomes during gut transit and once they are released back to the soil as casts. To address this knowledge gap, we used 16S rRNA next-generation sequencing to characterize the microbiomes of soil, gut and casts from the earthworm Aporrectodea caliginosa. We also studied whether these three microbiomes are clearly distinct in composition or can be merged into metacommunities. A large proportion of bacteria was unique to each microbiome—soil (82%), gut (89%) and casts (75%), which indicates that the soil microbiome is greatly modified during gut transit. The three microbiomes also differed in alpha diversity, which peaked during gut transit and decreased in casts. Furthermore, gut transit also modified the structure of the soil microbiome, which clustered away from those of the earthworm gut and cast samples. However, this clustering pattern was not supported by metacommunity analysis, which indicated that soil and gut samples make up one metacommunity and cast samples another. These results have important implications for understanding the dynamics of soil microbial communities and nutrient cycles. Full article
(This article belongs to the Special Issue Soil Microbial Diversity and Its Ecological Functions)
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13 pages, 3761 KiB  
Article
Bacterial Communities of Forest Soils along Different Elevations: Diversity, Structure, and Functional Composition with Potential Impacts on CO2 Emission
by Wanlong Sun, Zhouyuan Li, Jiesi Lei and Xuehua Liu
Microorganisms 2022, 10(4), 766; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10040766 - 01 Apr 2022
Cited by 10 | Viewed by 2470
Abstract
Soil bacteria are important components of forest ecosystems, there compostion structure and functions are sensitive to environmental conditions along elevation gradients. Using 16S rRNA gene amplicon sequencing followed by FAPROTAX function prediction, we examined the diversity, composition, and functional potentials of soil bacterial [...] Read more.
Soil bacteria are important components of forest ecosystems, there compostion structure and functions are sensitive to environmental conditions along elevation gradients. Using 16S rRNA gene amplicon sequencing followed by FAPROTAX function prediction, we examined the diversity, composition, and functional potentials of soil bacterial communities at three sites at elevations of 1400 m, 1600 m, and 2200 m in a temperate forest. We showed that microbial taxonomic composition did not change with elevation (p = 0.311), though soil bacterial α-diversities did. Proteobacteria, Acidobacteria, Actinobacteria, and Verrucomicrobia were abundant phyla in almost all soil samples, while Nitrospirae, closely associated with soil nitrogen cycling, was the fourth most abundant phylum in soils at 2200 m. Chemoheterotrophy and aerobic chemoheterotrophy were the two most abundant functions performed in soils at 1400 m and 1600 m, while nitrification (25.59% on average) and aerobic nitrite oxidation (19.38% on average) were higher in soils at 2200 m. Soil CO2 effluxes decreased (p < 0.050) with increasing elevation, while they were positively correlated (r = 0.55, p = 0.035) with the abundances of bacterial functional groups associated with carbon degradation. Moreover, bacterial functional composition, rather than taxonomic composition, was significantly associated with soil CO2 effluxes, suggesting a decoupling of taxonomy and function, with the latter being a better predictor of ecosystem functions. Annual temperature, annual precipitation, and pH shaped (p < 0.050) both bacterial taxonomic and functional communities. By establishing linkages between bacterial taxonomic communities, abundances of bacterial functional groups, and soil CO2 fluxes, we provide novel insights into how soil bacterial communities could serve as potential proxies of ecosystem functions. Full article
(This article belongs to the Special Issue Soil Microbial Diversity and Its Ecological Functions)
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14 pages, 2011 KiB  
Article
Diversity of Microbial Communities of Pinus sylvestris var. mongolica at Spatial Scale
by Dan-Dan Wang, Wen Zhao, Mumin Reyila, Kai-Chuan Huang, Shun Liu and Bao-Kai Cui
Microorganisms 2022, 10(2), 371; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10020371 - 05 Feb 2022
Cited by 10 | Viewed by 2023
Abstract
Soil microorganisms play an indispensable role in the forest ecosystem. It is necessary to study the soil microorganisms in Pinus sylvestris var. mongolica, which is one of the afforestation species widely planted in the northern sandy region of China. We collected soil [...] Read more.
Soil microorganisms play an indispensable role in the forest ecosystem. It is necessary to study the soil microorganisms in Pinus sylvestris var. mongolica, which is one of the afforestation species widely planted in the northern sandy region of China. We collected soil samples of P. sylvestris at large spatial scales and analyzed bacterial and fungal community composition differences using high-throughput sequencing techniques. The results showed that: (1) the richness index of different sandy lands was significantly different. The α-diversity of bacteria was the highest in Mu Us Sandy Land, and the α-diversity of fungi was the highest in Horqin Sandy Land. (2) The dominant phyla of bacteria were Actinobacteria, Proteobacteria, Chloroflexi and Acidobacteria, while the dominant phyla of fungi were Ascomycota and Basidiomycota. The relative abundance of dominant phyla was different. (3) Temperature and precipitation were the main driving factors of bacterial and fungal community change at large spatial scale. In addition, bacteria were also affected by total nitrogen, soil organic carbon and pH content; fungal community was affected by pH. The microorganisms showed obvious differences in geographical distribution, which could provide ideas for promoting sustainable management of P. sylvestris stand. Full article
(This article belongs to the Special Issue Soil Microbial Diversity and Its Ecological Functions)
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12 pages, 1424 KiB  
Article
Contrasting Patterns and Drivers of Soil Fungal Communities between Two Ecosystems Divided by the Treeline
by Xueying Wang, Guixiang Li, Yuxin Zhang and Keming Ma
Microorganisms 2021, 9(11), 2280; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9112280 - 02 Nov 2021
Cited by 1 | Viewed by 1330
Abstract
The treeline is a sensitive region of the terrestrial ecosystem responding to climate change. However, studies on the composition and formation mechanisms of soil fungal communities across the treeline are still lacking. In this study, we investigated the patterns of soil fungal community [...] Read more.
The treeline is a sensitive region of the terrestrial ecosystem responding to climate change. However, studies on the composition and formation mechanisms of soil fungal communities across the treeline are still lacking. In this study, we investigated the patterns of soil fungal community composition and interactions among functional guilds above and below the treeline using Illumina high-throughput sequencing and ecological network analysis. The results showed that there were significant differences in the soil environment and soil fungal community composition between the two ecosystems above and below the treeline. At the local scale of this study, geographic distance and environmental factors affected the composition of the soil fungal community. Soil temperature was an important environmental predictor of soil fungal community composition. Species in soil fungal communities in the subalpine meadow were more closely related to each other compared to those in the montane forest. Furthermore, the soil fungal community in montane forest was more stable. Our findings contribute to a better understanding of how mountain ecological functions respond to global climate change. Full article
(This article belongs to the Special Issue Soil Microbial Diversity and Its Ecological Functions)
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