Fine-scale diversity patterns in belowground microbial communities are consistent across kingdoms

ABSTRACT The belowground environment is heterogeneous and complex at fine spatial scales. Physical structures, biotic components and abiotic conditions create a patchwork mosaic of potential niches for microbes. Questions remain about mechanisms and patterns of community assembly belowground, including: Do fungal and bacterial communities assemble differently? How do microbes reach the roots of host plants? Within a 4 m2 plot in alpine vegetation, high throughput sequencing of the 16S (bacteria) and ITS1 (fungal) ribosomal RNA genes was used to characterise microbial community composition in roots and adjacent soil of a viviparous host plant (Bistorta vivipara). At fine spatial scales, beta-diversity patterns in belowground bacterial and fungal communities were consistent, although compositional change was greater in bacteria than fungi. Spatial structure and distance-decay relationships were also similar for bacteria and fungi, with significant spatial structure detected at <50 cm among root- but not soil-associated microbes. Recruitment of root microbes from the soil community appeared limited at this sampling and sequencing depth. Possible explanations for this include recruitment from low-abundance populations of soil microbes, active recruitment from neighbouring plants and/or vertical transmission of symbionts to new clones, suggesting varied methods of microbial community assembly for viviparous plants. Our results suggest that even at relatively small spatial scales, deterministic processes play a significant role in belowground microbial community structure and assembly.

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Disentangling Responses of the Subsurface Microbiome to Wetland Status and Implications for Indicating Ecosystem Functions

Microorganisms ◽

10.3390/microorganisms9020211 ◽

2021 ◽

Vol 9 (2) ◽

pp. 211

Author(s):

Jie Gao ◽

Miao Liu ◽

Sixue Shi ◽

Ying Liu ◽

Yu Duan ◽

...

Keyword(s):

Microbial Community ◽

High Throughput Sequencing ◽

Carbon Fixation ◽

Microbial Community Composition ◽

Ecosystem Functions ◽

Microbial Composition ◽

Wetland Ecosystems ◽

Soil Microbial ◽

Geochemical Properties ◽

Microbial Groups

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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Importance of spatially structured environmental heterogeneity in controlling microbial community composition at small spatial scales in an agricultural field

Soil Biology and Biochemistry ◽

10.1016/j.soilbio.2009.06.003 ◽

2009 ◽

Vol 41 (9) ◽

pp. 1833-1840 ◽

Cited By ~ 57

Author(s):

Rima B. Franklin ◽

Aaron L. Mills

Keyword(s):

Microbial Community ◽

Community Composition ◽

Environmental Heterogeneity ◽

Spatial Scales ◽

Microbial Community Composition ◽

Agricultural Field

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Consistent predictors of microbial community composition across scales in grasslands reveal low context-dependency

10.1101/2021.11.29.470306 ◽

2021 ◽

Author(s):

Dajana Radujković ◽

Sara Vicca ◽

Margaretha van Rooyen ◽

Peter Wilfahrt ◽

Leslie Brown ◽

...

Keyword(s):

Microbial Community ◽

Community Composition ◽

Spatial Scales ◽

Regional Scale ◽

Microbial Community Composition ◽

Soil Microbial Communities ◽

Plant Productivity ◽

Context Dependency ◽

Fungal Community Composition ◽

Soil Microbial

Environmental circumstances shaping soil microbial communities have been studied extensively, but due to disparate study designs it has been difficult to resolve whether a globally consistent set of predictors exists, or context-dependency prevails. Here, we used a network of 18 grassland sites (11 sampled across regional plant productivity gradients) to examine i) if the same abiotic or biotic factors predict both large- and regional-scale patterns in bacterial and fungal community composition, and ii) if microbial community composition differs consistently with regional plant productivity (low vs high) across different sites. We found that there is high congruence between predictors of microbial community composition across spatial scales; bacteria were predominantly associated with soil properties and fungi with plant community composition. Moreover, there was a microbial community signal that clearly distinguished high and low productivity soils that was shared across worldwide distributed grasslands suggesting that microbial assemblages vary predictably depending on grassland productivity.

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Microbiota community assembly in wild rice (Oryza longistaminata) in response to drought stress shows phylogenetic conservation, stochasticity, and aboveground-belowground patterns

10.21203/rs.3.rs-40339/v1 ◽

2020 ◽

Author(s):

xia ding ◽

Xiaojue Peng ◽

Zhichao Chen ◽

Yingjie Li ◽

Lihui Mao ◽

...

Keyword(s):

Microbial Community ◽

Drought Stress ◽

Microbial Communities ◽

Community Assembly ◽

Wild Rice ◽

Microbial Community Composition ◽

Α Diversity ◽

Oryza Longistaminata ◽

Network Properties ◽

Microbiome Assembly

Abstract Background Drought is a global environmental stress that limits crop yields. Microbial communities control many biogeochemical processes, and a predictive understanding of how crop microbial communities assemble in response to drought stress is central to addressing the challenges caused by drought. Little is known about the microbiome assembly processes in rice-ecosystems, particularly with regard to their environmental adaptation. Wild rice may serve as a source of superior drought tolerance candidate for rice breeding. There is an urgent need to explore wild rice resistance mechanisms to drought stress. Here, we evaluated the effect of drought stress on the microbial community recruitment and assembly in the endosphere (leaf, stem, and root) and rhizosphere of Oryza longistaminata. Results Species replacement was the dominant process shaping microbial community composition under drought stress. O. longistaminata recruited the phyla Actinobacteria and Fusobacteria, the genus Streptomyces, and phototrophic prokaryotes to improve its fitness. The host exerted strong effects on microbiome assembly, and the responses of the microbial community structure to the drought environment showed above- and belowground patterns. Drought reduced taxonomic α-diversity and destabilized co-occurrence network properties in the leaves and stems, but not in the roots and rhizosphere. Drought promoted the restructuring and strengthening of belowground network links to more strongly interconnect network properties. The drought response of the microbiome was phylogenetically conserved. Stochastic (neutral) processes acted on microbial community reassembly in response to drought stress across all four compartments. Conclusions Our results provide new insight into the mechanisms through which drought alters microbial community assembly in drought-tolerant wild rice and reveal a potential strategy for manipulating plant microbiomes to improve crop fitness.

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High-Throughput Sequencing Approach to Analyze the Effect of Aging Time and Barrel Usage on the Microbial Community Composition of Red Wines

Frontiers in Microbiology ◽

10.3389/fmicb.2020.562560 ◽

2020 ◽

Vol 11 ◽

Author(s):

Dimitrios Kioroglou ◽

Albert Mas ◽

Maria C. Portillo

Keyword(s):

Microbial Community ◽

Aging Time ◽

Community Composition ◽

High Throughput ◽

High Throughput Sequencing ◽

Microbial Community Composition ◽

Red Wines

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Seasonal Variation in the Rhizosphere and Non-Rhizosphere Microbial Community Structures and Functions of Camellia yuhsienensis Hu

Microorganisms ◽

10.3390/microorganisms8091385 ◽

2020 ◽

Vol 8 (9) ◽

pp. 1385

Author(s):

Jun Li ◽

Ziqiong Luo ◽

Chenhui Zhang ◽

Xinjing Qu ◽

Ming Chen ◽

...

Keyword(s):

Seasonal Variation ◽

Microbial Community ◽

High Throughput Sequencing ◽

Sulfur Metabolism ◽

Pathogen Resistance ◽

High Yield ◽

Glutathione Metabolism ◽

Oilseed Crop ◽

Soil Microbial ◽

Bacteria And Fungi

Camellia yuhsienensis Hu, endemic to China, is a predominant oilseed crop, due to its high yield and pathogen resistance. Past studies have focused on the aboveground parts of C. yuhsienensis, whereas the microbial community of the rhizosphere has not been reported yet. This study is the first time to explore the influence of seasonal variation on the microbial community in the rhizosphere of C. yuhsienensis using high-throughput sequencing. The results showed that the dominant bacteria in the rhizosphere of C. yuhsienensis were Chloroflexi, Proteobacteria, Acidobacteria, Actinobacteria, and Planctomycetes, and the dominant fungi were Ascomycota, Basidiomycota, and Mucoromycota. Seasonal variation has significant effects on the abundance of the bacterial and fungal groups in the rhizosphere. A significant increase in bacterial abundance and diversity in the rhizosphere reflected the root activity of C. yuhsienensis in winter. Over the entire year, there were weak correlations between microorganisms and soil physiochemical properties in the rhizosphere. In this study, we found that the bacterial biomarkers in the rhizosphere were chemoorganotrophic Gram-negative bacteria that grow under aerobic conditions, and fungal biomarkers, such as Trichoderma, Mortierella, and Lecanicillium, exhibited protection against pathogens in the rhizosphere. In the rhizosphere of C. yuhsienensis, the dominant functions of the bacteria included nitrogen metabolism, oxidative phosphorylation, glycine, serine and threonine metabolism, glutathione metabolism, and sulfur metabolism. The dominant fungal functional groups were endophytes and ectomycorrhizal fungi of a symbiotroph trophic type. In conclusion, seasonal variation had a remarkable influence on the microbial communities and functions, which were also significantly different in the rhizosphere and non-rhizosphere of C. yuhsienensis. The rhizosphere of C. yuhsienensis provides suitable conditions with good air permeability that allows beneficial bacteria and fungi to dominate the soil microbial community, which can improve the growth and pathogen resistance of C. yuhsienensis.

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Correction to: Contrast diversity patterns and processes of microbial community assembly in a river-lake continuum across a catchment scale in northwestern China

Environmental Microbiome ◽

10.1186/s40793-020-00360-z ◽

2020 ◽

Vol 15 (1) ◽

Author(s):

Xiangming Tang ◽

Guijuan Xie ◽

Keqiang Shao ◽

Yang Hu ◽

Jian Cai ◽

...

Keyword(s):

Microbial Community ◽

Community Assembly ◽

Northwestern China ◽

Catchment Scale ◽

Diversity Patterns ◽

Patterns And Processes ◽

Microbial Community Assembly

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Soil Microbial Community Assembly and Interactions Are Constrained by Nitrogen and Phosphorus in Broadleaf Forests of Southern China

Forests ◽

10.3390/f11030285 ◽

2020 ◽

Vol 11 (3) ◽

pp. 285 ◽

Cited By ~ 1

Author(s):

Mengxin Zhao ◽

Jing Cong ◽

Jingmin Cheng ◽

Qi Qi ◽

Yuyu Sheng ◽

...

Keyword(s):

Microbial Community ◽

Community Composition ◽

Community Assembly ◽

Soil Microbial Community ◽

Southern China ◽

Microbial Community Composition ◽

Nitrogen And Phosphorus ◽

Soil Microbial ◽

Microbial Community Assembly ◽

Microbial Functional Gene

Subtropical and tropical broadleaf forests play important roles in conserving biodiversity and regulating global carbon cycle. Nonetheless, knowledge about soil microbial diversity, community composition, turnover and microbial functional structure in sub- and tropical broadleaf forests is scarce. In this study, high-throughput sequencing was used to profile soil microbial community composition, and a micro-array GeoChip 5.0 was used to profile microbial functional gene distribution in four sub- and tropical broadleaf forests (HS, MES, HP and JFL) in southern China. The results showed that soil microbial community compositions differed dramatically among all of four forests. Soil microbial diversities in JFL were the lowest (5.81–5.99) and significantly different from those in the other three forests (6.22–6.39). Furthermore, microbial functional gene interactions were the most complex and closest, likely in reflection to stress associated with the lowest nitrogen and phosphorus contents in JFL. In support of the importance of environmental selection, we found selection (78–96%) dominated microbial community assembly, which was verified by partial Mantel tests showing significant correlations between soil phosphorus and nitrogen content and microbial community composition. Taken together, these results indicate that nitrogen and phosphorus are pivotal in shaping soil microbial communities in sub- and tropical broadleaf forests in southern China. Changes in soil nitrogen and phosphorus, in response to plant growth and decomposition, will therefore have significant changes in both microbial community assembly and interaction.

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