scholarly journals Relative Importance of Deterministic and Stochastic Processes on Soil Microbial Community Assembly in Temperate Grasslands

2021 ◽  
Vol 9 (9) ◽  
pp. 1929
Author(s):  
Nana Liu ◽  
Huifeng Hu ◽  
Wenhong Ma ◽  
Ye Deng ◽  
Qinggang Wang ◽  
...  
Keyword(s):  
Stochastic Processes ◽  
Soil Microbes ◽  
Explanatory Power ◽  
Soil Microbial Communities ◽  
Northern China ◽  
Temperate Grasslands ◽  
Soil Layers ◽  
Soil Microbial ◽  
Β Diversity ◽  
Deterministic Processes

Changes in species composition across communities, i.e., β-diversity, is a central focus of ecology. Compared to macroorganisms, the β-diversity of soil microbes and its drivers are less studied. Whether the determinants of soil microbial β-diversity are consistent between soil depths and between abundant and rare microorganisms remains controversial. Here, using the 16S-rRNA of soil bacteria and archaea sampled at different soil depths (0–10 and 30–50 cm) from 32 sites along an aridity gradient of 1500 km in the temperate grasslands in northern China, we compared the effects of deterministic and stochastic processes on the taxonomic and phylogenetic β-diversity of soil microbes. Using variation partitioning and null models, we found that the taxonomic β-diversity of the overall bacterial communities was more strongly determined by deterministic processes in both soil layers (the explanatory power of environmental distance in topsoil: 25.4%; subsoil: 47.4%), while their phylogenetic counterpart was more strongly determined by stochastic processes (the explanatory power of spatial distance in topsoil: 42.1; subsoil 24.7%). However, in terms of abundance, both the taxonomic and phylogenetic β-diversity of the abundant bacteria in both soil layers was more strongly determined by deterministic processes, while those of rare bacteria were more strongly determined by stochastic processes. In comparison with bacteria, both the taxonomic and phylogenetic β-diversity of the overall abundant and rare archaea were strongly determined by deterministic processes. Among the variables representing deterministic processes, contemporary and historical climate and aboveground vegetation dominated the microbial β-diversity of the overall and abundant microbes of both domains in topsoils, but soil geochemistry dominated in subsoils. This study presents a comprehensive understanding on the β-diversity of soil microbial communities in the temperate grasslands in northern China. Our findings highlight the importance of soil depth, phylogenetic turnover, and species abundance in the assembly processes of soil microbial communities.

scholarly journals Comparative study on microbial community structure across orchard soil, cropland soil, and unused soil

2017 ◽  
Vol 12 (No. 4) ◽  
pp. 237-245 ◽  
Author(s):  
C. Cheng ◽  
D. Zhao ◽  
D. Lv ◽  
S. Li ◽  
G. Du
Keyword(s):  
Land Use ◽  
Microbial Communities ◽  
Functional Diversity ◽  
Soil Microbes ◽  
Soil Microbial Communities ◽  
Polymer Composition ◽  
Soil Conditions ◽  
Soil Layers ◽  
Soil Microbial ◽  
Orchard Soil

We examined the effects of three different soil conditions (orchard soil, cropland soil, unused soil) on the functional diversity of soil microbial communities. The results first showed that orchard and cropland land use significantly changed the distribution and diversity of soil microbes, particularly at surface soil layers. The richness index (S) and Shannon diversity index (H) of orchard soil microbes were significantly higher than the indices of the cropland and unused soil treatments in the 0–10 cm soil layer, while the S and H indices of cropland soil microbes were the highest in 10–20 cm soil layers. Additionally, the Simpson dominance index of cropland soil microbial communities was the highest across all soil layers. Next, we found that carbon source differences in soil layers under the three land use conditions can mainly be attributed to their carbohydrate and polymer composition, indicating that they are the primary cause of the functional differences in microbial communities under different land uses. In conclusion, orchard and cropland soil probably affected microbial distribution and functional diversity due to differences in vegetation cover, cultivation, and management measures.

scholarly journals Effects of Soil Microbes on Forest Recovery to Climax Community through the Regulation of Nitrogen Cycling

Forests ◽  
2020 ◽  
Vol 11 (10) ◽  
pp. 1027
Author(s):  
Dandan Qi ◽  
Fujuan Feng ◽  
Yanmei Fu ◽  
Ximei Ji ◽  
Xianfa Liu
Keyword(s):  
Relative Abundance ◽  
Soil Microbes ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
N Cycling ◽  
Forest Recovery ◽  
Forest Types ◽  
Ecosystem Recovery ◽  
Soil Microbial ◽  
Clear Cutting

Microbes, as important regulators of ecosystem processes, play essential roles in ecosystem recovery after disturbances. However, it is not clear how soil microbial communities and functions change and affect forest recovery after clear-cutting. Here, we used metagenome sequencing to systematically analyse the differences in soil microbial community composition, functions, and nitrogen (N) cycling pathways between primary Korean pine forests (PF) and secondary broad-leaved forests (SF) formed after clear-cutting. Our results showed that the dominant phyla of the two forest types were consistent, but the relative abundance of some phyla was significantly different. Meanwhile, at the genus level, the fold-changes of rare genera were larger than the dominant and common genera. The genes related to microbial core metabolic functions, virulence factors, stress response, and defence were significantly enriched in SF. Additionally, based on the relative abundance of functional genes, a schema was proposed to analyse the differences in the whole N cycling processes between the two forest types. In PF, the stronger ammoniation and dissimilatory nitrate reduction (DNRA) and the weaker nitrification provided a genetic explanation for PF dominated by ammonium (NH4+) rather than nitrate (NO3−). In SF, the weaker DNRA, the stronger nitrification and denitrification, the higher soil available phosphorus (AP), and the lower nitrogen to phosphorus ratio (N/P) comprehensively suggested that SF was faced with a greater degree of N limitation. These results offer insights into the potential relationship between soil microbes and forest recovery, and aid in implementing proper forestry management.

scholarly journals Vertebrate Decomposition Is Accelerated by Soil Microbes

2014 ◽  
Vol 80 (16) ◽  
pp. 4920-4929 ◽  
Author(s):  
Christian L. Lauber ◽  
Jessica L. Metcalf ◽  
Kyle Keepers ◽  
Gail Ackermann ◽  
David O. Carter ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Soil Microbes ◽  
Soil Microbial Communities ◽  
Natural Phenomenon ◽  
Rrna Gene ◽  
Data Set ◽  
Soil Microbial ◽  
Decomposer Community ◽  
Carrion Decomposition

ABSTRACTCarrion decomposition is an ecologically important natural phenomenon influenced by a complex set of factors, including temperature, moisture, and the activity of microorganisms, invertebrates, and scavengers. The role of soil microbes as decomposers in this process is essential but not well understood and represents a knowledge gap in carrion ecology. To better define the role and sources of microbes in carrion decomposition, lab-reared mice were decomposed on either (i) soil with an intact microbial community or (ii) soil that was sterilized. We characterized the microbial community (16S rRNA gene for bacteria and archaea, and the 18S rRNA gene for fungi and microbial eukaryotes) for three body sites along with the underlying soil (i.e., gravesoils) at time intervals coinciding with visible changes in carrion morphology. Our results indicate that mice placed on soil with intact microbial communities reach advanced stages of decomposition 2 to 3 times faster than those placed on sterile soil. Microbial communities associated with skin and gravesoils of carrion in stages of active and advanced decay were significantly different between soil types (sterile versus untreated), suggesting that substrates on which carrion decompose may partially determine the microbial decomposer community. However, the source of the decomposer community (soil- versus carcass-associated microbes) was not clear in our data set, suggesting that greater sequencing depth needs to be employed to identify the origin of the decomposer communities in carrion decomposition. Overall, our data show that soil microbial communities have a significant impact on the rate at which carrion decomposes and have important implications for understanding carrion ecology.

Effects of xeric shrubs on soil microbial communities in a desert in northern China

2016 ◽  
Vol 414 (1-2) ◽  
pp. 281-294 ◽  
Author(s):  
Yanfei Sun ◽  
Yuqing Zhang ◽  
Wei Feng ◽  
Shugao Qin ◽  
Zhen Liu ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Northern China ◽  
Soil Microbial

scholarly journals Pesticides effect on soil microbial ecology and enzyme activity- An overview

2016 ◽  
Vol 8 (2) ◽  
pp. 1126-1132 ◽  
Author(s):  
Sanjay Arora ◽  
Divya Sahni
Keyword(s):  
Microbial Biomass ◽  
Soil Microbial Biomass ◽  
Soil Microbes ◽  
Microbial Biomass Carbon ◽  
Soil Microbial Communities ◽  
Field Application ◽  
Microbial Biomass C ◽  
Microbial Biomass Nitrogen ◽  
Soil Microbial ◽  
Chemical Pesticides

In modern agriculture, chemical pesticides are frequently used in agricultural fields to increase crop production. Besides combating insect pests, these insecticides also affect the activity and population of beneficial soil microbial communities. Chemical pesticides upset the activities of soil microbes and thus may affect the nutritional quality of soils. This results in serious ecological consequences. Soil microbes had different response to different pesticides. Soil microbial biomass that plays an important role in the soil ecosystem where they have crucial role in nutrient cycling. It has been reported that field application of glyphosate increased microbial biomass carbon by 17% and microbial biomass nitrogen by 76% in nine soils at 14 days after treatment. The soil microbial biomass C increased significantly upto 30 days in chlorpyrifos as well as cartap hydrochloride treated soil, but thereafter decreased progressively with time. Soil nematodes, earthworms and protozoa are affected by field application rates of the fungicide fenpropimorph and other herbicides. Thus, there is need to assess the effect of indiscriminate use of pesticides on soil microorganisms, affecting microbial activity and soil fertility.

scholarly journals Soil fungal networks are more sensitive to grazing exclusion than bacterial networks

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9986
Author(s):  
Lingling Chen ◽  
Jiajia Shi ◽  
Zhihua Bao ◽  
Taogetao Baoyin
Keyword(s):  
Soil Microbial Communities ◽  
Northern China ◽  
Desert Steppe ◽  
Plant Composition ◽  
Negative Effects ◽  
Grazing Exclusion ◽  
Soil Microbial ◽  
Lack Of Information ◽  
Soil Fungal Community ◽  
Management Issues

Soil microbial communities play a crucial role in ecological restoration, but it is unknown how co-occurrence networks within these communities respond to grazing exclusion. This lack of information was addressed by investigating the effects of eight years of grazing exclusion on microbial networks in an area of Stipa glareosa P. Smirn desert steppe in northern China. Here, we show that fungal networks were more sensitive to grazing exclusion than bacterial networks. Eight years of grazing exclusion decreased the soil fungal community stability via changes in plant composition and reductions in soil total organic carbon, in this case triggering negative effects on the S. glareosa desert steppe. The results provide new insights into the response mechanisms of soil microbes to grazing exclusion and offer possible solutions for management issues in the restoration of degraded desert steppe.

scholarly journals Soil Bacterial and Fungal Composition and Diversity Responses to Seasonal Deer Grazing in a Subalpine Meadow

Diversity ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 84
Author(s):  
Andéole Niyongabo Turatsinze ◽  
Baotian Kang ◽  
Tianqi Zhu ◽  
Fujiang Hou ◽  
Saman Bowatte
Keyword(s):  
Relative Abundance ◽  
Soil Microbial Communities ◽  
Gansu Province ◽  
Total Carbon ◽  
Mountain Range ◽  
Microbial Composition ◽  
Soil Microbial ◽  
Β Diversity ◽  
Α Diversity ◽  
Soil Bacterial

Soil microbial composition and diversity are widely recognized for their role in ecological functioning. This study examined the differences of soil microbial communities between two seasonally grazed grasslands. The study area was in the Gansu red deer farm located on the Qilian Mountain range in the Gansu province of northwestern China. This farm adopted a seasonal rotation grazing system whereby grasslands at higher altitudes are grazed in summer (SG), whilst grasslands at lower altitudes are grazed in winter (WG). The soil bacterial and fungal communities were examined by Illumina MiSeq sequencing. We found that soil water content (SWC), organic carbon (OC), total carbon (TC), and total nitrogen (TN) were significantly higher, whereas the C/N ratio was significantly lower in SG than WG pastures. The α-diversity of bacteria was greater than that of fungi in both pastures, while both bacterial and fungal α-diversity were not significantly different between the pastures. The bacterial β-diversity was significantly different between the pastures, but fungal β-diversity was not. The bacterial phylum Actinobacteria and fungal phylum Ascomycota were dominant in both pastures. The relative abundance of Actinobacteria in soil was significantly higher in WG pastures, whereas the relative abundance of Proteobacteria in soil was significantly higher in SG pastures. Significant correlations between bacterial and fungal phyla and soil properties were observed, but this varied between the two grasslands. This study showed that distinct microbial community structures developed in two pastures within the same geographic location that were grazed in different seasons.

scholarly journals Inhibition of select actinobacteria by the organophosphate pesticide chlorpyrifos

2021 ◽  
Author(s):  
Nathan D. McDonald ◽  
Courtney E. Love ◽  
Rushyannah Killens-Cade ◽  
Jason Werth ◽  
Matthew Gebert ◽  
...  
Keyword(s):  
Soil Microbes ◽  
Organophosphorus Compounds ◽  
Crop Protection ◽  
Soil Microbial Communities ◽  
Soil Microbiome ◽  
Transient Effects ◽  
Soil Microbial ◽  
Agricultural Pesticides ◽  
Solid Media

ABSTRACTOrganophosphorus compounds have an extensive history as both agricultural pesticides as well as chemical nerve agents. Decades of research have demonstrated numerous links between these chemicals and their direct and indirect effects on humans and other organisms. The inhibitory effects of organophosphate pesticides (OPPs) on metazoan physiology, are well-characterized; however, the effects of organophosphorus compounds on soil microbes - essential contributors to key agricultural processes - are poorly understood. Chlorpyrifos (CPF) is an OPP that is used globally for crop protection. Studies of CPF application to soils have shown transient effects on soil microbial communities with conflicting data. Here, we directly test the effect of CPF on a panel of 196 actinobacteria strains, examining the effects of CPF on their growth and in vitro phenotypes on solid media. Strains were grown and replica-plated onto media containing CPF or a vehicle control and grown at 28°C. CPF dramatically inhibited the growth of most strains and/or altered colony morphologies, with 13 strains completely inhibited by CPF. In disk diffusion assays with CPF, its degradation product 3,5,6-trichloropyridinol (TCP), malathion, parathion, monocrotophos and mevinphos, only CPF exhibited direct antimicrobial activity suggesting that the observed effects were due to CPF itself.IMPORTANCEChlorpyrifos is a globally used pesticide with documented neurological effects on non-target organisms in the environment. Finding that chlorpyrifos can inhibit the growth of some soil microbes in vitro may have implications for the composition, stability, and health of the soil microbiome. Due to the importance of soil microbes to numerous biogeochemical processes in agricultural systems, additional investigations into the non-target effects of CPF on soil microbes are clearly needed.

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