Effect of Long-Term Cropping Systems on the Diversity of the Soil Bacterial Communities

Soil microbial communities are involved in the maintenance of productivity and health of agricultural systems; therefore an adequate understanding of soil biodiversity plays a key role in ensuring sustainable use of soil. In the present study, we evaluated the influence of different cropping systems on the biodiversity of the soil bacterial communities, based on a 54-year field experiment established in Martonvásár, Hungary. Terminal restriction fragment length polymorphism (T-RFLP) fingerprinting technique was used to assess soil bacterial diversity and community structure in maize monoculture and three different crop rotations (maize–alfalfa, maize–wheat and the maize–barley–peas–wheat Norfolk type). No differences in richness and diversity were detected between maize monoculture and crop rotations except for the most intense rotation system (Norfolk-type). Although the principal component analysis did not reveal a clear separation between maize monoculture and the other rotation systems, the pairwise tests of analysis of similarity (ANOSIM) revealed that there are significant differences in the composition of bacterial communities between the maize monoculture and maize–alfalfa rotation as well as between wheat–maize and Norfolk-type rotation.

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Neutral processes and high inter-annual turnover shape the assembly of soil bacterial communities in a Mediterranean watershed

10.1101/542076 ◽

2019 ◽

Author(s):

Myrto Tsiknia ◽

Stilianos Fodelianakis ◽

Nikolaos P. Nikolaidis ◽

Nikolaos V. Paranychianakis

Keyword(s):

Stochastic Processes ◽

Microbial Communities ◽

Bacterial Communities ◽

Ecosystem Functioning ◽

Soil Microbial Communities ◽

Soil Bacterial Communities ◽

Environmental Selection ◽

Mediterranean Landscapes ◽

Soil Bacterial ◽

Annual Turnover

AbstractThere is a renewed interest in recent years on the ecological processes (stochastic vs selective) driving the assembly of microbial communities. Such information could potentially improve our understanding on ecosystem functioning and resilience to disturbances, ecosystem response to environmental shifts, and adoption of sustainable soil management practices. Herein, employing a suite of existing methodologies, we show that stochastic processes have an important role on the assembly of soil bacterial communities at a Mediterranean watershed. Moreover, we document that the relative contribution of assembly processes varies over the years. The observed intensification of stochastic processes was accompanied by a decrease in the contribution of variable selection in favor of homogeneous selection and dispersal and this trend was only marginally affected by land use (natural vs agricultural lands) or soil depth. Our study also revealed a high inter-annual turnover of soil microbial communities that was likely stimulated by the weak environmental selection and the prevailing environmental conditions (drying-wetting cycles) in Mediterranean landscapes, implying potential impacts on ecosystem functioning and our ability to predict soil response to environmental shifts. Using nitrogen mineralization rate (NMR) as a representative function we document highly variable NMR over the sampling years, land uses and soil depths and lack of significant associations with the monitored environmental variables and individual taxa. In summary, our study provides novel insights on the organization and functioning of microbial communities at Mediterranean ecosystems and sets directions towards a more advanced understanding of the relationships among environmental factors, microbial community structure, and ecosystem functioning that could contribute to sustainable management of these severely degraded ecosystems.

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Impact of Maize–Mushroom Intercropping on the Soil Bacterial Community Composition in Northeast China

Agronomy ◽

10.3390/agronomy10101526 ◽

2020 ◽

Vol 10 (10) ◽

pp. 1526

Author(s):

Xiaoqin Yang ◽

Yang Wang ◽

Luying Sun ◽

Xiaoning Qi ◽

Fengbin Song ◽

...

Keyword(s):

Bacterial Communities ◽

Northeast China ◽

Management Practice ◽

Bacterial Community Composition ◽

Soil Microbial Communities ◽

Chemical Properties ◽

Crop Productivity ◽

Rrna Gene ◽

Soil Bacterial Communities ◽

Soil Bacterial

Conservative agricultural practices have been adopted to improve soil quality and maintain crop productivity. An efficient intercropping of maize with mushroom has been developed in Northeast China. The objective of this study was to evaluate and compare the effects of planting patterns on the diversity and structure of the soil bacterial communities at a 0–20 cm depth in the black soil zone of Northeast China. The experiment consisted of monoculture of maize and mushroom, and intercropping in a split-plot arrangement. The characteristics of soil microbial communities were performed by 16S rRNA gene amplicom sequencing. The results showed that intercropping increased soil bacterial richness and diversity compared with maize monoculture. The relative abundances of Acidobacteria, Chloroflexi, Saccharibacteria and Planctomycetes were significantly higher, whereas Proteobacteria and Firmicutes were lower in intercropping than maize monoculture. Redundancy analysis suggested that pH, NO3−-N and NH4+-N contents had a notable effect on the structure of the bacterial communities. Moreover, intercropping significantly increased the relative abundance of carbohydrate metabolism pathway functional groups. Overall, these findings demonstrated that intercropping of maize with mushroom strongly impacts the physical and chemical properties of soil as well as the diversity and structure of the soil bacterial communities, suggesting this is a sustainable agricultural management practice in Northeast China.

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Soil bacterial communities in three rice-based cropping systems differing in productivity

Scientific Reports ◽

10.1038/s41598-020-66924-8 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Min Huang ◽

Alin Tian ◽

Jiana Chen ◽

Fangbo Cao ◽

Yumei Chen ◽

...

Keyword(s):

Bacterial Communities ◽

Cropping Systems ◽

Soil Bacterial Communities ◽

Soil Bacterial

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Dynamics of Bacterial Communities in a 30-Year Fertilized Paddy Field under Different Organic–Inorganic Fertilization Strategies

Agronomy ◽

10.3390/agronomy9010014 ◽

2019 ◽

Vol 9 (1) ◽

pp. 14 ◽

Cited By ~ 10

Author(s):

Yadong Yang ◽

Peixin Wang ◽

Zhaohai Zeng

Keyword(s):

Bacterial Community ◽

Bacterial Communities ◽

Soil Microbial Communities ◽

Hierarchical Cluster ◽

Organic Manure ◽

Community Structures ◽

Long Term Effects ◽

Inorganic Fertilizers ◽

Soil Bacterial Communities ◽

Soil Bacterial

Fertilization plays important roles in improving soil fertility and in increasing crop yield. Soil microbial communities are sensitive indicators of soil quality and health, which could be affected by fertilization strategy. However, our knowledge on how organic–inorganic fertilizers application affects soil bacterial communities remains largely poorly understood. In this study, we investigated the long-term effects of different organic–inorganic fertilization strategies: without fertilizer (CK), fertilizers NPK (CF), fertilizers NPK, plus 30% organic manure (CFM1), and fertilizers NPK plus 60% organic manure (CFM2) on soil bacterial communities in paddy fields. Results showed that the bacterial 16S ribosomal DNA (rDNA) gene abundances in treatments CF, CFM1, and CFM2 were 1.44, 1.54, and 1.28 times higher than that in CK and the ACE index in treatment CFM1 was 9.0% greater than that in treatment CFM2, respectively. Fertilization strategy significantly changed the relative abundance of Nitrospirae, Gemmatimonadetes, and unclassified bacteria at the phylum level and bacteria belonging to order Nitrospira, candidate bacterium SBR2076, unclassified bacteria, Syntrophobacterales, and Solibacterales at the order level, respectively. High organic–inorganic fertilizer application rates inhibited the growth of Nitrospirae by 20–35%, and stimulated the growth of Gemmatimonadetes by 14–77%, relative to the rest of the treatments, respectively. Hierarchical cluster and principal coordinate analysis (PCoA) showed that the fertilization strategy affected the bacterial community structures, and the organic–inorganic fertilized treatments possessed similar bacterial community structures. Furthermore, soil pH, total nitrogen (TN), and soil organic carbon (SOC) were the main driving factors altering the bacterial communities. Our results suggested that combined organic–inorganic fertilizers application increased soil nutrient contents and bacterial abundances, and this could be an optimized fertilization strategy in regulating soil bacterial communities for rice production.

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Impact of Land Use on Bacterial Diversity and Community Structure in Temperate Pine and Indigenous Forest Soils

Diversity ◽

10.3390/d11110217 ◽

2019 ◽

Vol 11 (11) ◽

pp. 217 ◽

Cited By ~ 1

Author(s):

Adenike Eunice Amoo ◽

Olubukola Oluranti Babalola

Keyword(s):

Land Use ◽

Microbial Communities ◽

Bacterial Diversity ◽

Correspondence Analysis ◽

Canonical Correspondence Analysis ◽

Bacterial Communities ◽

Soil Microbial Communities ◽

Soil Characteristics ◽

Soil Bacterial Communities ◽

Soil Bacterial

Soil microbial communities are an important part of ecosystems that possess the capability to improve ecosystem services; however, several aspects of the ecology of forest soil bacterial communities are still unknown. Here, we investigated the impact of land-use change on soil bacterial communities and the soil characteristics. High-throughput sequencing was used to ascertain the bacterial diversity and canonical correspondence analysis was used to determine relationships between the bacterial communities and environmental variables. Our results show spatial heterogeneity in the distribution of the microbial communities and significant relationships between the microbes and soil characteristics (axis 1 of the canonical correspondence analysis (CCA) plot explained 64.55% of the total variance while axis 2 described 24.49%). Knowledge of this is essential as it has direct consequences for the functioning of the soil ecosystem.

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Soil Type Is the Primary Determinant of the Composition of the Total and Active Bacterial Communities in Arable Soils

Applied and Environmental Microbiology ◽

10.1128/aem.69.3.1800-1809.2003 ◽

2003 ◽

Vol 69 (3) ◽

pp. 1800-1809 ◽

Cited By ~ 480

Author(s):

Martina S. Girvan ◽

Juliet Bullimore ◽

Jules N. Pretty ◽

A. Mark Osborn ◽

Andrew S. Ball

Keyword(s):

Land Use ◽

Organic Matter ◽

Soil Type ◽

Bacterial Communities ◽

Management Practices ◽

Bacterial Community Composition ◽

Arable Soils ◽

Soil Biodiversity ◽

Soil Bacterial Communities ◽

Soil Bacterial

ABSTRACT Degradation of agricultural land and the resulting loss of soil biodiversity and productivity are of great concern. Land-use management practices can be used to ameliorate such degradation. The soil bacterial communities at three separate arable farms in eastern England, with different farm management practices, were investigated by using a polyphasic approach combining traditional soil analyses, physiological analysis, and nucleic acid profiling. Organic farming did not necessarily result in elevated organic matter levels; instead, a strong association with increased nitrate availability was apparent. Ordination of the physiological (BIOLOG) data separated the soil bacterial communities into two clusters, determined by soil type. Denaturing gradient gel electrophoresis and terminal restriction fragment length polymorphism analyses of 16S ribosomal DNA identified three bacterial communities largely on the basis of soil type but with discrimination for pea cropping. Five fields from geographically distinct soils, with different cropping regimens, produced highly similar profiles. The active communities (16S rRNA) were further discriminated by farm location and, to some degree, by land-use practices. The results of this investigation indicated that soil type was the key factor determining bacterial community composition in these arable soils. Leguminous crops on particular soil types had a positive effect upon organic matter levels and resulted in small changes in the active bacterial population. The active population was therefore more indicative of short-term management changes.

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Cover Cropping Impacts Soil Microbial Communities and Functions in Mango Orchards

Agriculture ◽

10.3390/agriculture11040343 ◽

2021 ◽

Vol 11 (4) ◽

pp. 343

Author(s):

Zhiyuan Wei ◽

Quanchao Zeng ◽

Wenfeng Tan

Keyword(s):

Bacterial Diversity ◽

Fungal Diversity ◽

Soil Microbial Communities ◽

Soil Bacterial Diversity ◽

Mango Fruit ◽

Soil Biodiversity ◽

Soil Microbial ◽

Cover Cropping ◽

Soil Bacterial ◽

Soil Fungal Diversity

Soil microbes play critical roles in nutrient cycling, net primary production, food safety, and climate change in terrestrial ecosystems, yet their responses to cover cropping in agroforestry ecosystems remain unknown. Here, we conducted a field experiment to assess how changes in cover cropping with sown grass strips affect the fruit yields and quality, community composition, and diversity of soil microbial taxa in a mango orchard. The results showed that two-year cover cropping increased mango fruit yields and the contents of soluble solids. Cover cropping enhanced soil fungal diversity rather than soil bacterial diversity. Although cover cropping had no significant effects on soil bacterial diversity, it significantly influenced soil bacterial community compositions. These variations in the structures of soil fungal and bacterial communities were largely driven by soil nitrogen, which positively or negatively affected the relative abundance of both bacterial and fungal taxa. Cover cropping also altered fungal guilds, which enhanced the proportion of pathotrophic fungi and decreased saprotrophic fungi. The increase in fungal diversity and alterations in fungal guilds might be the main factors to consider for increasing mango fruit yields and quality. Our results indicate that cover cropping affects mango fruit yields and quality via alterations in soil fungal diversity, which bridges a critical gap in our understanding of the linkages between soil biodiversity and fruit quality in response to cover cropping in orchard ecosystems.

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Effects of Imazapyr on Spartina alterniflora and Soil Bacterial Communities in a Mangrove Wetland

Water ◽

10.3390/w13223277 ◽

2021 ◽

Vol 13 (22) ◽

pp. 3277

Author(s):

Xue Mo ◽

Panpan Dong ◽

Lumeng Xie ◽

Yujiao Xiu ◽

Yanqi Wang ◽

...

Keyword(s):

Bacterial Diversity ◽

Spartina Alterniflora ◽

Bacterial Communities ◽

Available Phosphorus ◽

Soil Bacterial Diversity ◽

Factors Affecting ◽

Soil Bacterial Communities ◽

Mangrove Wetland ◽

Significant Difference ◽

Soil Bacterial

The invasion of Spartina alterniflora (S. alterniflora) has caused serious damage to coastal wetland ecosystems in China, especially the mangrove wetlands in South China. This study aimed to validate the effect of imazapyr on S. alterniflora and soil. The controlled experiment was conducted in May 2021 at the Zhangjiangkou Mangrove Wetland Reserve. In the experiment, 25% (W) imazapyr was used, and six treatments were set up: 3035, 6070, and 9105 mL/acre 25% imazapyr and 1299, 2604, and 5202 mL/acre of AGE 809 + 6070 mL/acre 25% imazapyr. The results showed no side effects on mangrove plants in the spraying area. The highest control efficiency (95.9%) was given by 2604 mL/acre of AGE 809 + 6070 mL/acre 25% imazapyr. The residues of imazapyr in different soils were reduced to 0.10–0.59 mg/kg. The sequencing results showed no significant difference in the overall bacterial communities under different treatments (p > 0.05). The soil bacterial diversity in the samples with adjuvant was higher than that in the samples without adjuvant, while the abundance values were the opposite. There were 10 main communities (>0.3%) at phylum level in all soil samples, among which Proteobacteria, Bacteroidetes, Acidobacteria, Chloflexi, and Actinobacteria were the dominant communities, and the latter four’s abundance changed significantly (p < 0.05). There were significant abundance differences between the groups of oligotrophic and eutrophic bacteria. The redundancy analysis and Monte Carlo tests showed that the total organic carbon (TOC), total phosphorus (TP), available phosphorus (AP), ammonia nitrogen, and total nitrogen were the main factors affecting soil bacterial diversity. At the same time, TOC, AP, and TP were the most critical factors affecting the overall characteristics of soil bacterial communities in different treatments, while soil residues had no significant effect on bacteria. This might be due to the addition and degradation of imazapyr and the coverage of S. alterniflora. The best recommendation is 2604 mL/acre of AGE 809 + 6070 mL/acre 25% imazapyr to be applied in China’s mangrove wetland reserves and coastal wetlands.

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The role of ecosystem engineers in shaping the diversity and function of arid soil bacterial communities

SOIL ◽

10.5194/soil-7-611-2021 ◽

2021 ◽

Vol 7 (2) ◽

pp. 611-637

Author(s):

Capucine Baubin ◽

Arielle M. Farrell ◽

Adam Št'ovíček ◽

Lusine Ghazaryan ◽

Itamar Giladi ◽

...

Keyword(s):

Community Composition ◽

Bacterial Communities ◽

Soil Microbial Communities ◽

Ecosystem Engineers ◽

Patch Type ◽

Arid Soil ◽

Soil Bacterial Communities ◽

Ant Nests ◽

Soil Bacterial ◽

And Function

Abstract. Ecosystem engineers (EEs) are present in every environment and are known to strongly influence ecological processes and thus shape the distribution of species and resources. In this study, we assessed the direct and indirect effect of two EEs (perennial shrubs and ant nests), individually and combined, on the composition and function of arid soil bacterial communities. To that end, topsoil samples were collected in the Negev desert highlands during the dry season from four patch types: (1) barren soil; (2) under shrubs; (3) near ant nests; or (4) near ant nests situated under shrubs. The bacterial community composition and potential functionality were evaluated in the soil samples (14 replicates per patch type) using 16S rRNA gene amplicon sequencing together with physico-chemical measures of the soil. We have found that the EEs affected the community composition differently. Barren patches supported a soil microbiome, dominated by Rubrobacter and Proteobacteria, while in EE patches Deinococcus-Thermus dominated. The presence of the EEs similarly enhanced the abundance of phototrophic, nitrogen cycle, and stress-related genes. In addition, the soil characteristics were altered only when both EEs were combined. Our results suggest that arid landscapes foster unique communities selected by patches created by each EE(s), solo or in combination. Although the communities' composition differs, they support similar potential functions that may have a role in surviving the harsh arid conditions. The combined effect of the EEs on soil microbial communities is a good example of the hard-to-predict non-additive features of arid ecosystems that merit further research.

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The role of ecosystem engineers in shaping the diversity and function of arid soil bacterial communities

10.5194/soil-2021-29 ◽

2021 ◽

Author(s):

Capucine Baubin ◽

Arielle M. Farrell ◽

Adam Šťovíček ◽

Lusine Ghazaryan ◽

Itamar Giladi ◽

...

Keyword(s):

Community Composition ◽

Bacterial Communities ◽

Soil Microbial Communities ◽

Ecosystem Engineers ◽

Patch Type ◽

Arid Soil ◽

Soil Bacterial Communities ◽

Ant Nests ◽

Soil Bacterial ◽

And Function

Abstract. Ecosystem engineers (EEs) are present in every environment and are known to strongly influence ecological processes and thus shape the distribution of species and resources. In this study, we assessed the direct and indirect effect of two EEs (perennial shrubs and ant nests), individually and combined, on the composition and function of arid soil bacterial communities. To that end, topsoil samples were collected in the Negev Desert Highlands during the dry season from four patch types: (1) barren soil; (2) under shrubs; (3) near ant nests; or (4) near ant nests situated under shrubs. The bacterial community composition and potential functionality were evaluated in the soil samples (fourteen replicates per patch type) using 16S rRNA gene amplicon sequencing, together with physico-chemical measures of the soil. We have found that the EEs differently affected the community composition. Barren patches supported a soil microbiome, dominated by Rubrobacter and Proteobacteria, while in EE patches Deinococcus-Thermus dominated. The presence of the EEs similarly enhanced the abundance of phototrophic, nitrogen cycle and stress- related genes. In addition, the soil characteristics were altered only when both EEs were combined. Our results suggest that arid landscapes foster unique bacterial communities selected by patches created by each EE(s), solo or in combination. Although, the communities’ composition differs, they support similar potential functions that may have a role in surviving harsh arid conditions. The combined effect of the EEs on soil microbial communities is a good example of hard to predict non-additive features of arid ecosystems that, therefore, merit further research.

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