Community Assembly and Co-occurrence Patterns Underlying the Core and Satellite Bacterial Sub-communities in the Tibetan Lakes
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ABSTRACT:
SUBMITTER: Yan Q
PROVIDER: S-EPMC8567192 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BACKGROUND:Household biogas digesters are widely used to harvest energy in rural areas of developing countries. Understanding core prokaryotic communities, their co-occurrence patterns, and their relationships to environmental factors is important to manage these small-scale anaerobic digestion systems effectively. In this study, 43 household biogas digesters were collected across eight provinces in China. Prokaryotic communities were investigated using 454 pyrosequencing of 16S rRNA genes. RESULTS:Fourteen core genera and ten core OTUs were identified in household biogas digesters. They were mainly affiliated with the phylum Firmicutes, Synergistetes, Actinobacteria, Chloroflexi, and Spirochaetes. Core prokaryotic genera were mainly composed of Clostridium, Clostridium XI, Syntrophomonas, Cloacibacillus, Sedimentibacter, and Turicibacter. Prokaryotic communities in the 43 samples were clearly divided into two clusters. Cluster I was dominated by Clostridium, while Cluster II was dominated by members of Spirochaetes, Bacteroidales, Clostridia, and abundant syntrophs and methanogens. NH4 (+)-N and COD contributed significantly to the assembly of the prokaryotic community in Cluster I, while NH4 (+)-N, pH, and phosphate contributed significantly to Cluster II. Correlation-based network analysis showed that the prokaryotic communities in the biogas digesters were dominated by some functional modules. Cluster I was dominated by acetotrophic methanogenic modules and the Clostridium-driven primary fermentation module, while the network of Cluster II was dominated by hydrogenotrophic and acetogenic methanogenesis modules and multi-group-driven (Spirochaetes, Bacteroidales, and Clostridia) primary fermentation modules. The network of Cluster II was more complex and functionally redundant. CONCLUSIONS:Prokaryotic communities identified in the household biogas digesters varied significantly and were affected by environmental factors, such as NH4 (+)-N, pH, and COD. However, core prokaryotic communities existed, and most of them were also dominant populations. Cosmopolitan OTUs tended to co-occur. Prokaryotic communities in biogas digesters were well organized by some functional modules. The modular structure of the prokaryotic community, which has functional redundancy, enhances the resistance against environmental stress and maintains digestion efficiency in the anaerobic digestion process.
| S-EPMC4582640 | biostudies-literature
Project description:Understanding how species interaction and assembly processes structure the abundant and rare bacterial biospheres in soils is crucial for predicting how biodiversity influences ecosystem functioning. Here, we profiled the bacterial communities across a salt marsh ecosystem gradient to investigate the co-occurrence patterns across taxa and the relative influence of ecological processes mediating the assembly of the abundant and rare biospheres in soil. Our results revealed abundant taxa to be ubiquitous across all sites, whereas the distributions of the rare taxa were relatively more site specific. The α-diversity indices and β-diversity of rare subcommunities were significantly higher than those of the abundant subcommunities. Besides, both the taxonomic and functional composition of soil bacterial communities differed significantly between the two biospheres. Furthermore, the influence of stochasticity differed in each subcommunity. In particular, stochastic processes were relatively more important in constraining the assembly of rare taxa. Co-occurrence network analysis revealed that a few abundant taxa occupy central nodes within the networks, possibly indicating crucial roles as keystone taxa. Collectively, these findings suggest that abundant and rare bacterial biospheres have distinct distributions underpinned by a dynamic interplay of ecological processes and taxon co-occurrence patterns.IMPORTANCE Estuarine salt marshes are highly productive ecosystems subjected to regular disturbances by hydrodynamic exchange. However, little is known about how distinct assembly processes and co-occurrence of taxa influence the structure of the abundant and rare bacterial biospheres in these soil systems. This study aims at unravelling these intricacies by studying a typical estuarine salt marsh located in Hangzhou Bay, China. Our study provides important pieces of evidence on the diverse distribution of rare and abundant bacterial biospheres. We show that a few abundant taxa are central nodes in species co-occurrence, potentially playing important roles as keystone species in the system. In addition, we highlight a dynamic interplay of assembly processes structuring these two subcommunities.
| S-EPMC7301849 | biostudies-literature
Project description:Co-occurrence networks allow for the identification of potential associations among species, which may be important for understanding community assembly and ecosystem functions. We employed this strategy to examine prokaryotic co-occurrence patterns in the Amazon soils and the response of these patterns to land use change to pasture, with the hypothesis that altered microbial composition due to deforestation will mirror the co-occurrence patterns across prokaryotic taxa. In this study, we calculated Spearman correlations between operational taxonomic units (OTUs) as determined by 16S rRNA gene sequencing, and only robust correlations were considered for network construction (-0.80 ? P ? 0.80, adjusted P < 0.01). The constructed network represents distinct forest and pasture components, with altered compositional and topological features. A comparative analysis between two representative modules of these contrasting ecosystems revealed novel information regarding changes to metabolic pathways related to nitrogen cycling. Our results showed that soil physicochemical properties such as temperature, C/N and H++Al3+ had a significant impact on prokaryotic communities, with alterations to network topologies. Taken together, changes in co-occurrence patterns and physicochemical properties may contribute to ecosystem processes including nitrification and denitrification, two important biogeochemical processes occurring in tropical forest systems.
| S-EPMC6294608 | biostudies-literature
Project description:Exploring large environmental datasets generated by high-throughput DNA sequencing technologies requires new analytical approaches to move beyond the basic inventory descriptions of the composition and diversity of natural microbial communities. In order to investigate potential interactions between microbial taxa, network analysis of significant taxon co-occurrence patterns may help to decipher the structure of complex microbial communities across spatial or temporal gradients. Here, we calculated associations between microbial taxa and applied network analysis approaches to a 16S rRNA gene barcoded pyrosequencing dataset containing >160?000 bacterial and archaeal sequences from 151 soil samples from a broad range of ecosystem types. We described the topology of the resulting network and defined operational taxonomic unit categories based on abundance and occupancy (that is, habitat generalists and habitat specialists). Co-occurrence patterns were readily revealed, including general non-random association, common life history strategies at broad taxonomic levels and unexpected relationships between community members. Overall, we demonstrated the potential of exploring inter-taxa correlations to gain a more integrated understanding of microbial community structure and the ecological rules guiding community assembly.
| S-EPMC3260507 | biostudies-literature
Project description: Not available
| S-EPMC3960547 | biostudies-literature
Project description:The VIA Classification on character strengths and virtues suggests 24 character strengths clustered into six core virtues (wisdom and knowledge, courage, humanity, justice, temperance, and transcendence). Three recent studies employed different methods for testing the assignment of character strengths to virtues (e.g., expert and layperson ratings), and generally supported the VIA classification. However, the co-occurrence of character strengths and virtues within individuals has not been examined yet. Another untested assumption is that an individual's composition of character strengths is related to being considered of "good character." Thus, the present study addresses three research questions: (1) How do character strengths and measured virtues co-occur within individuals? (2.1) How does the number of character strengths an individual possesses within a virtue cluster relate to their level of the respective virtue? (2.2) How does the composition of an individual's character strengths relate to being considered of "good character"? We combined data from different studies to obtain a sample of N = 1,241 participants (n = 897 self-raters, n = 344 informant-raters, 70.1% female) aged 18 to 92 years (M = 30.64). All participants completed assessments of character strengths and virtues. Regarding (1), we found a high convergence of the correlations between strengths and virtues and the VIA Classification: 22 out of 24 character strengths correlated with the assigned virtue (exceptions were hope, which correlated highest with courage, and humor, which correlated highest with humanity). Also, 15 character strengths showed the numerically highest correlation with their assigned virtue. Regarding (2.1), overall, we found a linear trend between the number of strengths within one cluster and the virtue level. Regarding (2.2), we found higher levels of reported "good character" in those who possessed either (a) at least one character strength in each virtue cluster or (b) all character strengths in at least one virtue compared to those who did not. The present results contribute to the discussion regarding the structure of character: individuals' character strengths relate to differences in virtues, across different measures and data sources. Relationships were mostly as expected, and deviations were consistent with results obtained using other approaches.
| S-EPMC7726161 | biostudies-literature
Project description:Strategies involving genes in the dehydration-responsive element binding (DREB) family, which participates in drought stress regulation, and intercropping with legumes are becoming prominent options in promoting sustainable sugarcane cultivation. An increasing number of studies focusing on root interactions in intercropping systems, particularly involving transgenic crops, are being conducted to better understand and thus, harness beneficial soil microbes to enhance plant growth. We designed experiments to investigate the characteristics of two intercropping patterns, soybean with wild-type (WT) sugarcane and soybean with genetically modified (GM) Ea-DREB2B-overexpressing sugarcane, to assess the response of the rhizosphere microbiota to the different cropping patterns. Bacterial diversity in the rhizosphere microbial community differed between the two intercropping pattens. In addition, the biomass of GM sugarcane that intercropped with soybean was significantly improved compared with WT sugarcane, and the aboveground biomass and root biomass of GM soybean intercropping sugarcane increased by 49.15 and 46.03% compared with monoculture. Furthermore, a beneficial rhizosphere environment for the growth of Actinobacteria was established in the systems intercropped with GM sugarcane. Improving the production mode of crops by genetic modification is a key strategy to improving crop yields and provides new opportunities to further investigate the effects of intercropping on plant roots and soil microbiota. Thus, this study provides a basis for selecting suitable sugarcane-soybean intercropping patterns and a theoretical foundation for a sustainable sugarcane production.
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Project description:Caves are typified by their permanent darkness and a shortage of nutrients. Consequently, bacteria play an important role in sustaining such subsurface ecosystems by dominating primary production and fueling biogeochemical cycles. China has one of the world's largest areas of karst topography in the Yunnan-Guizhou Plateau, yet the bacteriomes in these karst caves remain unexplored. In this study, bacteriomes of eight karst caves in southwest China were examined, and co-occurrence networks of cave bacterial communities were constructed. Results revealed abundant and diversified bacterial communities in karst caves, with Proteobacteria, Actinobacteria, and Firmicutes being the most abundant phyla. Statistical analysis revealed no significant difference in bacteriomes among the eight caves. However, a PCoA plot did show that the bacterial communities of 128 cave samples clustered into groups corresponding to sampling types (air, water, rock, and sediment). These results suggest that the distribution of bacterial communities is driven more by sample types than the separate caves from which samples were collected. Further community-level composition analysis indicated that Proteobacteria were most dominant in water and air samples, while Actinobacteria dominated the sediment and rock samples. Co-occurrence analysis revealed highly modularized assembly patterns of the cave bacterial community, with Nitrosococcaceae wb1-P19, an uncultured group in Rokubacteriales, and an uncultured group in Gaiellales, being the top-three keystone members. These results not only expand our understanding of cave bacteriomes but also inspires functional exploration of bacterial strains in karst caves.
| S-EPMC6691740 | biostudies-literature
Project description:Most glaciers in the Himalayas and the Tibetan Plateau are retreating, and glacier melt has been emphasized as the dominant driver for recent lake expansions on the Tibetan Plateau. By investigating detailed changes in lake extents and levels across the Tibetan Plateau from Landsat/ICESat data, we found a pattern of dramatic lake changes from 1970 to 2010 (especially after 2000) with a southwest-northeast transition from shrinking, to stable, to rapidly expanding. This pattern is in distinct contrast to the spatial characteristics of glacier retreat, suggesting limited influence of glacier melt on lake dynamics. The plateau-wide pattern of lake change is related to precipitation variation and consistent with the pattern of permafrost degradation induced by rising temperature. More than 79% of lakes we observed on the central-northern plateau (with continuous permafrost) are rapidly expanding, even without glacial contributions, while lakes fed by retreating glaciers in southern regions (with isolated permafrost) are relatively stable or shrinking. Our study shows the limited role of glacier melt and highlights the potentially important contribution of permafrost degradation in predicting future water availability in this region, where understanding these processes is of critical importance to drinking water, agriculture, and hydropower supply of densely populated areas in South and East Asia.
| S-EPMC4221193 | biostudies-literature
Project description:Thermokarst lakes are a ubiquitous and important landscape feature in cold regions and are changing tremendously due to the accelerated climate change. In thermokarst lakes, sediment and water are two distinct but highly interconnected habitats, harboring different bacterial communities in terms of taxonomic composition. However, the co-occurrence networks of these bacterial communities remain unclear. Here, we investigate the co-occurrence ecological networks of sediment and water bacterial communities for thermokarst lakes in the Yellow River Source Area on the Qinghai-Tibet Plateau. The results show that the bacterial communities construct distinct co-occurrence networks in sediment and water. The metacommunity network was parsed into four major modules formed by the operational taxonomic units (OTUs) enriched in sediment or water independently, and water-enriched OTUs exhibited much closer interconnections than sediment-enriched OTUs. When considering the sediment and water bacterial networks separately, different topological properties and modular patterns present: the sediment bacterial network was more clustered while the modules less responded to the environmental variables. On the contrary, the water bacterial network was more complex with the OTUs more interconnected and its modules more responded to the environmental variables. Moreover, the results of the structural equation model suggest that, by the influence of environmental variations on individual modules, the water bacterial communities would be more vulnerable under the fact of accelerating climate change. This study provides insights beyond a conventional taxonomic perspective, adding our knowledge of the potential mechanisms structuring bacterial community assembly and improving our prediction of the responses of this fast-changing ecosystem to future climate change.
| S-EPMC8569892 | biostudies-literature