Effects of Plants on Metacommunities and Correlation Networks of Soil Microbial Groups in an Ecologically Restored Wetland

In this study, we analyzed microbial community composition and the functional capacities of degraded sites and restored/natural sites in two typical wetlands of Northeast China—the Phragmites marsh and the Carex marsh, respectively. The degradation of these wetlands, caused by grazing or land drainage for irrigation, alters microbial community components and functional structures, in addition to changing the aboveground vegetation and soil geochemical properties. Bacterial and fungal diversity at the degraded sites were significantly lower than those at restored/natural sites, indicating that soil microbial groups were sensitive to disturbances in wetland ecosystems. Further, a combined analysis using high-throughput sequencing and GeoChip arrays showed that the abundance of carbon fixation and degradation, and ~95% genes involved in nitrogen cycling were increased in abundance at grazed Phragmites sites, likely due to the stimulating impact of urine and dung deposition. In contrast, the abundance of genes involved in methane cycling was significantly increased in restored wetlands. Particularly, we found that microbial composition and activity gradually shifts according to the hierarchical marsh sites. Altogether, this study demonstrated that microbial communities as a whole could respond to wetland changes and revealed the functional potential of microbes in regulating biogeochemical cycles.

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The influence of light on soil community structure and consequences for soil CO2, CO18O and COS exchange

10.5194/egusphere-egu2020-20422 ◽

2020 ◽

Author(s):

Lisa Wingate ◽

Clement Foucault ◽

Nicolas Fanin ◽

Joana Sauze ◽

Pierre-Alain Maron ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Soil Ph ◽

Isotope Composition ◽

Light Availability ◽

Alkaline Soils ◽

Soil Microbial ◽

Microbial Groups ◽

Taxonomic Groups ◽

Carbonyl Sulphide

The stable oxygen isotope composition of atmospheric CO2 and the mixing ratio of carbonyl sulphide (COS) are potential tracers of biospheric CO2 fluxes at large scales. However, the use of these tracers hinges on our ability to understand and better predict the activity of the enzyme carbonic anhydrase (CA) in different soil microbial groups, including phototrophs. Because different classes of the CA family (&#945;, &#946; and &#947;) may have different affinities to CO2 and COS and their expression should also vary between different microbial groups, differences in the community structure could impact the &#8216;community-integrated&#8217; CA activity differently for CO2 and COS. Four soils of different pH were incubated in the dark or with a diurnal cycle for forty days to vary the abundance of native phototrophs. Fluxes of CO2, CO18O and COS were measured to estimate CA activity alongside the abundance of bacteria, fungi and phototroph genes. The abundance of soil phototrophs increased most at higher soil pH. In the light, the strength of the soil CO2 sink and the CA-driven CO2-H2O isotopic exchange rates correlated with phototroph abundance. COS uptake rates were attributed to fungi whose abundance was positively enhanced in alkaline soils but only in the presence of increased phototrophs. In addition we developed a metabarcoding approach to reveal the interactions of specific taxonomic groups incuding photosynthetic eukaryotic algae and cyanobacteria when exposed to light and their impact on flux rates. Our findings demonstrate that soil-atmosphere CO2, COS and CO18O fluxes are strongly regulated by the microbial community structure in response to changes in soil pH and light availability and support the idea that different members of the microbial community express different classes of CA, with different affinities to CO2 and COS.

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Soil Microbial Activity and Diversity in Response to Soil Chemical Factors in Agricultural Soils

Journal of Tropical Soils ◽

10.5400/jts.2019.v24i1.43-51 ◽

2019 ◽

Vol 24 (1) ◽

pp. 43

Author(s):

Lily Ishak ◽

Philip Hugh Brown

Keyword(s):

Microbial Communities ◽

Agricultural Soils ◽

Soil Health ◽

Soil Microbial Communities ◽

Soil Microbial Activity ◽

Soil Microbial Diversity ◽

Soil Microbial ◽

Microbial Responses ◽

Chemical Factors ◽

Microbial Groups

The role of microbial communities in maintaining soil health is mostly influenced by chemical condition of soil. Microbial communities vary in response to soil chemical factors. The contradictive results from previous findings emphasise that it is difficult to define a pattern of the influence of soil chemical factors on soil microbial diversity and activity. The aim of the study was to assess soil microbial responses to soil chemical factors in agricultural soils. Composite soil (Dermosol order) samples taken from 16 commercial crop sites in Bundaberg, Queensland, Australia, were chemically and biologically analysed. It was found that bacterial and fungal activity and diversity were significantly affected by soil EC, SOM and NO3-N content, but were not influenced by soil pH, CEC, and Ca:Mg ratio. The diversity of bacterial and fungal communities displayed a positive linear relationship with soil EC, whereas the activity and diversity of these two microbial groups and SOM displayed a significant quadratic relationship. The finding suggested that microbial community was predominantly influenced by SOM content.

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Contrasting biogeographic patterns of bacterial and archaeal diversity in the top- and subsoils of temperate grasslands

10.1101/623264 ◽

2019 ◽

Author(s):

Nana Liu ◽

Huifeng Hu ◽

Wenhong Ma ◽

Ye Deng ◽

Yuqing Liu ◽

...

Keyword(s):

Climate Change ◽

Microbial Diversity ◽

Temperature Anomaly ◽

Soil Microbial Diversity ◽

Temperate Grasslands ◽

Diversity Patterns ◽

Biogeographic Patterns ◽

Soil Microbial ◽

Historical Temperature ◽

Microbial Groups

ABSTRACTBiogeographic patterns and drivers of soil microbial diversity have been extensively studied in the past few decades. However, most research has focused on the topsoil while the subsoil is assumed to have similar microbial diversity patterns as the topsoil. Here we compare patterns and drivers of microbial diversity in the top- (0-10 cm) versus subsoils (30-50 cm) of temperate grasslands in Inner Mongolia of China along an aridity gradient covering a ~1500-km transect from arid to mesic ecosystems. Counter to the conventional assumption, we find contrasting biogeographic patterns of diversity and influencing factors for different bacterial and archaeal groups and between depths. While bacterial diversity increases with increasing aridity, archaeal diversity decreases. Microbial diversity in the topsoil is most strongly influenced by aboveground vegetation, but is most strongly influenced by historical temperature anomaly since the Last Glacial Maximum (LGM) in the subsoil. Moreover, the biogeographic patterns of top-subsoil diversity difference varies for different microbial groups and is overall most strongly influenced by soil fertility difference between depths and historical temperature anomaly. These findings suggest that diversity patterns observed in the topsoil may not be readily applied to the subsoil horizons. For the subsoil in particular, historical climate plays a vital role in the distribution of various microbial groups. Overall, our study provides novel information for understanding and predicting soil microbial diversity patterns at depth.IMPORTANCEExploring the biogeographic patterns of soil microbial diversity is critical for understanding mechanisms underlying the response of soil processes to climate change. Using top- and subsoils from a ~1500-km temperature grassland transect, we find divergent patterns of microbial diversity and its determinants in the top-versus subsoils. Furthermore, we find important legacy effect of historical climate change on the microbial diversity of subsoil but not topsoil. Our findings challenge the conventional assumption of similar geographic patterns of soil microbial diversity along soil profiles and help to improve our understanding of how soil microbial communities may respond to future climate change in different regions with varied climate history.

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Responses of Soil Microbial Communities to Robinia Pseudoacacia Plantations of Different Ages in A Loess Area

10.20944/preprints201709.0016.v1 ◽

2017 ◽

Cited By ~ 1

Author(s):

Bingxue Zhang ◽

Rumeng Zhao ◽

Boyuan Bi ◽

Fengpeng Han

Keyword(s):

Soil Depth ◽

Robinia Pseudoacacia ◽

Principal Component ◽

Stand Age ◽

Soil Layers ◽

Loess Area ◽

Soil Microbial ◽

Different Ages ◽

Microbial Groups ◽

The Individual

Phospholipid fatty acids (PLFAs) can be used as biomarkers for qualitative and quantitative analyses of soil microbial community diversity. In this study, we collected soil samples at 10-cm intervals to a depth of 1 m from Robinia pseudoacacia plantations of four different ages (10, 15, 25 and 40 years) in a loess area and analysed the soil microbial community structure by PLFA analysis. A total of 97 PLFAs were detected in soils of R. pseudoacacia plantations of different ages. The individual PLFA contents gradually decreased in the 0- to 40-cm soil layers, with little variation in the 40- to 100-cm soil layers. The individual PLFAs were similarly distributed in the soils of R. pseudoacacia plantations of different ages, and there was a clear variation with stand age and soil depth. The individual PLFA contents in the 0- to 20-cm soil layers were highest for the 25-year-old plantation, while those in the 20- to 40-cm soil layers were relatively high for the 25- and 40-year-old plantations; the 16:0 content was the highest among individual PLFAs. The total PLFA content and the PLFA contents of different microbial groups [bacteria, fungi, Gram-positive bacteria (G+), Gram-negative bacteria (G-) and actinomycetes] initially increased before decreasing in the soils of R. pseudoacacia plantations with increasing stand age, whereas these contents gradually decreased with increasing soil depth; the highest PLFA contents was found in the 25-year-old plantation. The total PLFA content and the contents of fungal, G- and actinomycete PLFAs in the soils of R. pseudoacacia plantations differed significantly among stands of different ages in the 0- to 10-cm, 10- to 20-cm and 30- to 40-cm soil layers, while no significant differences were found in the 20- to 30-cm soil layers; the G+ and bacterial PLFAs contents in each of the 0- to 40-cm soil layers were significantly different. The PLFA ratios between different microbial groups differed among the stands of different ages. The fungi/bacteria ratio showed a “decrease-increase-decrease” trend with stand age, while the G+/G- ratio showed an “increase-decrease” trend. The saturated/monounsaturated PLFA ratio initially decreased before plateauing, while the opposite trend was observed for the cyclopropyl/precursor ratio. The PLFA contents of different microbial groups were ranked as follows: bacteria > G- > G+ > actinomycetes > fungi. In the principle component analysis, 18:1ω9c, 10Me18:0, i17:0, a17:0, 18:1ω7c, 18:1ω5c and 18:0 made the greatest contribution to principal component 1, and a14:0, i14:0 3OH, i14:0, i14:1ω7c and 14:0 made the greatest contribution to principal component 2. In conclusion, soil nutrient status and other soil eco-environmental stress factors should be considered in 10- to 25-year-old (particularly ~15-year-old) plots for the management of R. pseudoacacia plantations to prevent forest soil degradation and improve forest stand quality, thereby achieving better soil and water conservation and environmental improvement in R. pseudoacacia plantations.

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Allocation and turnover of rhizodeposited carbon in different soil microbial groups

Soil Biology and Biochemistry ◽

10.1016/j.soilbio.2020.107973 ◽

2020 ◽

Vol 150 ◽

pp. 107973 ◽

Cited By ~ 1

Author(s):

Junsheng Huang ◽

Weixing Liu ◽

Meifeng Deng ◽

Xin Wang ◽

Zhenhua Wang ◽

...

Keyword(s):

Soil Microbial ◽

Microbial Groups

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Effects of Long-term Cotton Continuous Cropping on Soil Microbiome

Scientific Reports ◽

10.1038/s41598-019-54771-1 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 4

Author(s):

Hui Xi ◽

Jili Shen ◽

Zheng Qu ◽

Dingyi Yang ◽

Shiming Liu ◽

...

Keyword(s):

Severe Disease ◽

Soil Microbial Communities ◽

Alpha Diversity ◽

Taxonomic Composition ◽

Soil Microbiome ◽

Continuous Cropping ◽

Bacterial Phyla ◽

Soil Microbial ◽

Microbial Groups

AbstractVerticillium wilt is a severe disease of cotton crops in Xinjiang and affecting yields and quality, due to the continuous cotton cropping in the past decades. The relationship between continuous cropping and the changes induced on soil microbiome remains unclear to date. In this study, the culture types of 15 isolates from Bole (5F), Kuitun (7F), and Shihezi (8F) of north Xinjiang were sclerotium type. Only isolates from field 5F belonged to nondefoliating pathotype, the others belonged to defoliating pathotype. The isolates showed pathogenicity differentiation in cotton. Fungal and bacterial communities in soils had some difference in alpha-diversity, relative abundance, structure and taxonomic composition, but microbial groups showed similarity in the same habitat, despite different sampling sites. The fungal phyla Ascomycota, and the bacterial phyla Proteobacteria, Actinobacteria, Chloroflexi, Acidobacteria and Gemmatimonadetes were strongly enriched. Verticillium abundance was significantly and positively correlated with AN, but negatively correlated with soil OM, AK and pH. Moreover, Verticillium was correlated in abundances with 5 fungal and 6 bacterial genera. Overall, we demonstrate that soil microbiome communities have similar responses to long-term continuous cotton cropping, providing new insights into the effects of continuous cotton cropping on soil microbial communities.

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Long-term biosolids application alters the composition of soil microbial groups and nutrient status in a pine plantation

Biology and Fertility of Soils ◽

10.1007/s00374-017-1219-8 ◽

2017 ◽

Vol 53 (7) ◽

pp. 799-809 ◽

Cited By ~ 5

Author(s):

Minhuang Wang ◽

Jianming Xue ◽

Jacqui Horswell ◽

Mark O. Kimberley ◽

Zhiqun Huang

Keyword(s):

Nutrient Status ◽

Pine Plantation ◽

Soil Microbial ◽

Microbial Groups ◽

Biosolids Application

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MICROBIOTA OF URBAN SOILS OF GREEN PLANTATIONS OF KYIV WITH THE ADDITION OF SILICON-CONTAINING COMPOUNDS

Odesa National University Herald Biology ◽

10.18524/2077-1746.2021.1(48).232843 ◽

2021 ◽

Vol 26 (1(48)) ◽

pp. 45-54

Author(s):

N. E., Ellanska ◽

O. P. Yunosheva

Keyword(s):

Functional Organization ◽

Soil Formation ◽

Urban Ecosystems ◽

Botanical Garden ◽

Trophic Relations ◽

Soil Microbial ◽

Natural Substances ◽

Microbiological Methods ◽

Before And After ◽

Microbial Groups

Problem. Intensive human pressure on urban ecosystems in big cities, such as Kyiv, leads to cenotic and trophic relations disbalance, agronomically useful microbiota and microfauna inhibition, plant resistance to any stressors decrease and disruption of normal soil formation. Therefore, it is important to find new effective, economically viable and environmentally safe methods to overcome soil sickness in city plantations. Aim. To study the structural and functional peculiarities of organization of soil microbial groups in anthropogenically disturbed zones of Kyiv green plantations in order to overcome soil fatigue with the use of natural substances - silicon-containing mineral analcime. Methods. Investigations were carried out on the basis of the National Botanical Garden M.M. Gryshko NAS of Ukraine, Department of Allelopathy. Six research regions in the most сontaminated and anthropogenically disturbed green areas of the Kyiv Obolonsky district were selected as objects. Twice a year, samples of root soil were taken at 0-20 cm depth before application (May) and 3.5 months after application of silicon-containing mixture (analcime) (September). The selection of soil samples, preparation and saving for the study of aerobic microbiota were carried out in accordance with ISO 10381-6-2001. The quantity of microorganisms of main ecological and trophic groups, direction of microbiological processes, identification of soil micromycetes were determined by conventional microbiological methods. Results. The results of this work showed that 3.5 months after the addition of the silicon-containing mixture, there were significant changes in the structure of the soil microbiocenosis. The increase in the number of microorganisms involved in the transformation of nitrogen compounds and the reduction of phytotoxic forms of soil fungi were detected, which indicates favorable conditions for the synthesis of humic compounds. The biggest changes were observed on the side of the highway with active emissions from automobiles and in the park, where higher content of iron ions was determined in the water for irrigation. Conclusions. The conducted research made it possible to estimate the structural and functional organization of microbial groups of the soils in a separate Kyiv district under different anthropogenic influence before and after the addition of silicon-containing mixture.

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Seasonal dynamics alters taxonomical and functional microbial profiles in Pampa biome soils under natural grasslands

10.7287/peerj.preprints.26569 ◽

2018 ◽

Author(s):

Anthony Barboza ◽

Victor S Pylro ◽

Rodrigo Jacques ◽

Paulo Gubiani ◽

Júlio Trindade ◽

...

Keyword(s):

Microbial Communities ◽

Seasonal Variations ◽

Soil Microbial Communities ◽

Soil Microbial ◽

Pampa Biome ◽

Natural Grasslands ◽

Microbial Groups ◽

Composition Changes ◽

New Strategies ◽

Selection Of

Soil microbial communities’ assembly is strongly tied to changes in temperature and moisture. Although microbial functional redundancy seems to overcome taxonomical composition changes, the sensitivity and resilience of soil microbial communities from subtropical regions in response to seasonal variations are still poorly understood. Thus, the development of new strategies for biodiversity conservation and sustainable management require a complete understanding of the soil abiotic process involved in the selection of microbial taxa and functions. In this work, we used state of the art molecular methodologies (Next Generation Sequencing) to compare the taxonomic (metataxonomics) and functional (metatranscriptomics) profiles among soil samples from two subtropical natural grasslands located in the Pampa biome, Brazil, in response to short-term seasonal variations. We found consistent effects of season on both microbial community structure and functions, but with the former being more influenced than the latter. These variations were more related to the oscillation in the relative abundances of specific taxa along seasons, rather than extinction and recolonization of taxa along seasons. In conclusion, the most abundant microbial groups and functions were shared between seasons and locations reflecting the existence of a stable taxonomical and functional core microbiota.

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