Biogeographic patterns of microbial association networks in paddy soil within Eastern China

Wan, Xiaoling; Gao, Qun; Zhao, Jianshu; Feng, Jiajie; Nostrand, Joy D. Van; Yang, Yunfeng; Zhou, Jizhong

doi:10.1016/j.soilbio.2019.107696

Cited by 75 publications

(44 citation statements)

References 76 publications

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“…This inference could be validated by a previous study showing that the biotic selection (species sorting) contributed more to microbial assembly processes than other forces in paddy soils [76]. Since methanogenesis is subject to distinct temperature filtering, the closer coexistence relationship of commonly coexisting taxa would appear with stronger niche occupation [77], consequently improving the efficiency of CH 4 production. In the future research, such coexistence relationship may be considered to add in climate warming model (e.g., GISS global climate models) to improve the accuracy of model prediction.…”

Section: Discussionmentioning

confidence: 54%

Coexistence patterns of soil methanogens are closely tied to methane generation and community assembly in rice paddies

Liu

Jiao

et al. 2021

Microbiome

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Background Soil methanogens participate in complex interactions, which determine the community structures and functions. Studies continue to seek the coexistence patterns of soil methanogens, influencing factors and the contribution to methane (CH4) production, which are regulated primarily by species interactions, and the functional significance of these interactions. Here, methane emissions were measured in rice paddies across the Asian continent, and the complex interactions involved in coexistence patterns of methanogenic archaeal communities were represented as pairwise links in co-occurrence networks. Results The network topological properties, which were positively correlated with mean annual temperature, were the most important predictor of CH4 emissions among all the biotic and abiotic factors. The methanogenic groups involved in commonly co-occurring links among the 39 local networks contributed most to CH4 emission (53.3%), much higher than the contribution of methanogenic groups with endemic links (36.8%). The potential keystone taxa, belonging to Methanobacterium, Methanocella, Methanothrix, and Methanosarcina, possessed high linkages with the methane generation functional genes mcrA, fwdB, mtbA, and mtbC. Moreover, the commonly coexisting taxa showed a very different assembly pattern, with ~ 30% determinism and ~ 70% stochasticity. In contrast, a higher proportion of stochasticity (93~99%) characterized the assembly of endemically coexisting taxa. Conclusions These results suggest that the coexistence patterns of microbes are closely tied to their functional significance, and the potential importance of common coexistence further imply that complex networks of interactions may contribute more than species diversity to soil functions.

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Section: Discussionmentioning

confidence: 54%

Coexistence patterns of soil methanogens are closely tied to methane generation and community assembly in rice paddies

Liu

Jiao

et al. 2021

Microbiome

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“…Raw sequencing data was processed through the inhouse pipeline (http://zhoulab5.rccc.ou.edu:8080/root) at University of Oklahoma, and the data processing procedures were documented in an earlier study (Wan et al 2020). In brief, chimeras and poor quality reads were removed using Uchime (Edgar et al 2011) and Brtim (Kong 2011), respectively.…”

Section: Dna Extraction Sequencing and Raw Data Processingmentioning

confidence: 99%

The intestinal microbiome of an Indo‐Pacific humpback dolphin (Sousa chinensis) stranded near the Pearl River Estuary, China

Wan

Cheng

et al. 2020

Integr. Zool.

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The mammalian intestinal microbiome is critical for host health and disease resistance. However, the cetacean intestinal microbiota remains relatively unexplored. By using high-throughput 16S rRNA gene sequencing, we analyzed intestinal bacterial samples from an Indo-pacific humpback dolphin (Sousa chinensis) stranded near the Pearl River Estuary in China. The samples included 3 anatomical regions (foregut, midgut, and rectum) and 2 anatomical locations (content and mucus). Our analyses revealed that the dolphin intestinal bacteria contained 139 operational taxonomic units (OTUs), dominated at the phyla level by Firmicutes (47.05% in the content; 94.77% in the mucus), followed by Bacteroidetes (23.63% in the content; 1.58% in the mucus) and Gammaproteobacteria (14.82% in the content; 2.05% in the mucus). The intestinal bacteria had a small core community (15 OTUs, accounting for 99.74% of the reads), some of which could be potentially pathogenic to both human and dolphins. As an alternative to sampling the dolphin intestinal bacteria, fecal sampling could be used. Additionally, function potentials such as, xenobiotics biodegradation, beta-lactam resistance, and human disease-related pathways, were detected in the dolphin intestinal bacteria. These findings provide the first baseline knowledge of the intestinal microbiome of the Indo-Pacific humpback dolphin, which may offer new insights into cetacean conservation by using microbial surveillance.

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“…Insights into microbial community structure can be obtained through building and analysing co‐occurrence topological networks when sufficient samples are available across spatial or temporal scales (Barberan et al., 2012; Faust et al., 2015). Ecological interactions are critical evolutionary forces for natural selection during the evolution of microbial communities (Chesson, 2000; Faust & Raes, 2012; Ma et al., 2020; Wan et al., 2020). The selective effects of biotic interactions on the spatial distribution of bacterial communities are generally ignored compared with the role of abiotic variables (Xiao et al., 2018).…”

Section: Discussionmentioning

confidence: 99%

Distinct microhabitats affect the relative balance of ecological processes shaping the spatial distribution of bacterial communities in lakeshore habitats

Zeng

et al. 2021

Freshwater Biology

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1. The lakeshore habitat, which is an interface zone between lake and land, harbours various organic particles providing nutrient-rich microhabitats for bacterial colonisation. Revealing the mechanisms maintaining the bacterial diversity generated on these particles is vital for understanding the biogeochemical processes within lakeshore habitats. To date, however, the bacterial communities within lakeshore habitats have been rarely explored, and knowledge of the ecological processes associated with their spatial distribution is limited.2. Here, we employed amplicon-based high throughput sequencing technology to investigate the composition, co-occurrence patterns, spatial distribution, and assembly processes of free-living and particle-attached bacterial communities (FLBC vs. PABC) across 29 lakeshore zones within freshwater lakes from two typical regions: Middle-Lower Yangtze River Plain and Yunnan-Kweichow Plateau.3. We found significant community dissimilarity between both bacterial lifestyles and regions. PABC exhibited higher community dissimilarity between the plain and plateau regions than FLBC did. Furthermore, eight operational taxonomic units were detected as a core bacterial community within the lakeshore habitats across the plain and plateau regions. Network analysis revealed that bacterial taxa preferring a particle-attached lifestyle exhibited more co-occurrence associations for both intra-and inter-community than the free-living lifestyle. Both FLBC and PABC showed significant distance-decay relationships in these two regions.Dispersal limitation was the most important process associated with patterns in the spatial distribution of FLBC and PABC, whereas the relative importance of variable and homogeneous selection differed between the assembly of FLBC and PABC because of differences in their microhabitats. 4. Our results highlight that dispersal limitation may be strongly associated with the spatial distribution of lakeshore bacterial communities at a regional scale.

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Biogeographic patterns of microbial association networks in paddy soil within Eastern China

Cited by 75 publications

References 76 publications

Coexistence patterns of soil methanogens are closely tied to methane generation and community assembly in rice paddies

Coexistence patterns of soil methanogens are closely tied to methane generation and community assembly in rice paddies

The intestinal microbiome of an Indo‐Pacific humpback dolphin (Sousa chinensis) stranded near the Pearl River Estuary, China

Distinct microhabitats affect the relative balance of ecological processes shaping the spatial distribution of bacterial communities in lakeshore habitats

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