Coordinated Metacommunity Assembly and Spatial Distribution of Multiple Microbial Kingdoms within a Lake

Water microecology is affected by seasons but not sediments: A spatiotemporal dynamics survey of bacterial community composition in Lake Changshou-The largest artificial lake in southwest China

This study aimed to evaluate the correlation between microecology of sediments and water as well as their spatial-temporal variations in Changshou Lake. The results demonstrated that microecology in the lake exhibits spatiotemporal heterogeneity, and microbial diversity of sediments was significantly higher than that of water body. Further, it was found that there was statistically insignificant positive correlation between microecology of sediments and that of water body. PCoA and community structure analysis revealed that the predominant phyla which exhibited significant spatial differences in sediments were Proteobacteria, Actinobacteria and Planctomycetes. While, the distribution of dominant bacteria Actinobacteria and Verrucomicrobia in water body showed significant seasonal differences. Microbial networks analysis indicated that there was a cooperative symbiotic relationship between lake microbial communities. Notably, the same bacterial genus had no significant positive correlation in sediment and water, which suggested that bacteria transport between sediment-water interface does not influence the microecological functions of lake water.

Determination of methanogenesis by nutrient availability via regulating the relative fitness of methanogens in anaerobic digestion

Response of microbial community to nutrient availability in anaerobic digestion (AD) remains elusive. Prokaryotic communities in AD batch cultures with 0, 1, 3, 5, 7, 11, 15, 20, and 25 g/L peptone were monitored using massive parallel sequencing and quantitative PCR over a 34-day experimental period. Methane production displayed a hump-shaped response to the nutrient gradient (peaking at 15 g/L peptone). Moreover, total and acetoclastic methanogens showed hump-shaped responses (both peaking at 11 g/L peptone). However, prokaryotic population increased with nutrient concentration (linear regression, R² = 0.86) while diversity decreased (R² = 0.94), and ordination analysis showed a gradual succession of community structure along the first axis. Network analysis revealed that extent of interspecific interactions (e.g., edge number and clustering coefficient) exhibited a hump-shaped response. The combined results indicate that abundant species became more dominated with increasing nutrient, which can result in a gain or loss of interspecific interaction within the community. Network module analysis showed that one module dominated the network at each nutrient level (comprising 41%-65% of the nodes), indicating that AD community formed a core microbial guild. The most abundant phylotypes, Macellibacteroides and Butyricicoccaceae, were consistently negative with acetoclastic methanogens in the dominant modules. Their predominance at ≥15 g/L peptone can explain the hump-shaped responses of methanogenesis and methanogens. Collectively, methanogenesis and microbial network exhibited hump-shaped responses, although microbial community exhibited monotonic responses. Therefore, nutrient availability can determine the methanogenesis through regulating the relative fitness of methanogens within the community.

Effects of dispersal on species distribution, abundance, diversity and interaction in a bacterial biofilm metacommunity

AIMS

Dispersal effects on biofilms have not been adequately studied despite their strong potential impacts on biofilm development. We investigated the effects of dispersal on biofilm metacommunity.

METHODS AND RESULTS

A bacterial consortium was allowed to form biofilms on 12 glass beads attached to disposable plates (compartmentalized or not), and biofilms were scrutinized on days 5, 10 and 15 using quantitative PCR and MiSeq sequencing. Biofilm population density was lesser by 2 orders of magnitude on day 5 when dispersal was allowed (p < 0.05). Then, the population rapidly increased by 4.4 orders with dispersal (p < 0.05) but did not change without dispersal. Community analyses revealed that dispersal increased the species diversity at all sampling times (p < 0.05). Dispersal affected the community structure and increased the homogeneity of local communities (p < 0.05). Distance-decay analysis showed that dispersal reduced the dissimilarity among local communities at all distance levels. Furthermore, dispersal reduced the variability of diversity, population and community structure. Network analysis revealed that dispersal increased the clustering coefficient, network density and connectivity.

CONCLUSIONS

Dispersal increased the species diversity, population and interaction and reduced the variability of the diversity, population and structure among local communities.

SIGNIFICANCE AND IMPACT OF STUDY

Our results suggest that dispersal can induce the niche complementarity and mass effects.

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

Plants may influence different aspects of the belowground microorganisms, including abundance, distribution, and interaction, in wetlands. Microbial communities were scrutinized in a 4-year-old restored wetland ecosystem with 5 distinct sites: a bare-soil site (10 local patches) and sites dominated by Miscanthus, Phragmites, Typha, and Zizania (20 patches per site). Ordination analysis revealed that plant-induced attributes (e.g., organic matter and total carbon and nitrogen) could explain the total environmental variance. Community comparisons showed that all groups (Bacteria, Fungi, Protista, and Metazoa) differed in community structure among the 5 sites (P < 0.05). Comparisons between the community and environmental ordination plots revealed that community structural variation among the sites correlated with the environmental change across all groups (R² ≥ 0.61). This indicates that all groups were primarily influenced by plant detritus. In addition, correlation networks markedly varied in topology and composition among the sites across all groups. There was a strong coupling between the metacommunity and correlation network for both Bacteria and Fungi (R² ≥ 0.58), indicating that the plants determined the spatial covariation patterns of microbial populations. Multi-group networks and group synchrony results revealed that Bacteria, Fungi, and Protista were synchronized with each other (R² ≥ 0.52) as the key founders of the microbial systems, while Metazoa participated in the system only under Miscanthus. Our findings concluded that the plants shaped the communities by controlling the abundance and interaction of their populations.

Spatial Variance of Species Distribution Predicts the Interspecies Interactions within a Microbial Metacommunity

Interspecies interactions have a profound influence on spatial distribution of coexisting microbial species. We explored whether spatial variance of species distribution (SVSD) predicts the degree of interspecies interactions within a microbial metacommunity. Simulations were used to determine the relationships from random, lake, soil, and biofilm metacommunity datasets (1,000 times). All of the bacterial datasets showed a negative correlation between the habitat breadth (inverse to SVSD) and the numbers of total, positive, and negative interspecies interactions (P < 0.05); the only exception was the relationship between habitat breadth and negative interactions in the biofilm dataset. The random dataset had no significant relationships (P > 0.05). We repeated the simulations to determine the degree of correlation and reproducibility (100 times). Habitat breadth was negatively correlated with the total and positive interactions in all of the real datasets (P < 0.05), and the negative relationships persisted across repetitions. Despite variability in the slope of total interactions, the slope values of positive interactions were similar for the real datasets (- 19.9, - 19.2, and - 25.8 for lake, soil, and biofilm, respectively). In conclusion, our results demonstrate the patterns of species interaction-distribution and show that interspecies interactions are positively correlated with the SVSD.

Local and Geographic Factors Shape the Occupancy-Frequency Distribution of Freshwater Bacteria

Species prevalence across the landscape is related to their local abundance, which is a result of deterministic and stochastic processes that select organisms capable of recolonizing sites where they were once extinct, a process known as the rescue effect. The occupancy-frequency distribution (OFD) describes these patterns and has been extensively used to understand organism's distribution but has been poorly tested on microorganisms. In order to test OFD on freshwater bacteria, we collected data from 60 shallow lakes distributed across a wide area in southeastern Brazil, to determine the bacterial operational taxonomic units (OTUs) that were present in all sites (core) and at only one site (satellite). Then, we analyzed the spatial abundance distributions of individual OTUs to understand the influence of local abundances on regional occupancy patterns. Finally, we tested the environmental factors that influenced occupancy and abundance. We found a significant bimodal OFD for freshwater bacteria using both OTUs (97% clustering) and amplicon sequence variants (ASVs, unique sequences), with 13 core OTUs and 1169 satellite OTUs, but only three core ASVs. Core organisms had a bimodal or gamma abundance distribution. The main driver of the core community was pH, while nutrients were key when the core community was excluded and the rest of the community (mild and satellite taxa) was considered. This study demonstrates the close relationship between local environmental conditions and the abundance and dispersion of microorganisms, which shapes their distribution across the landscape.

Covariation patterns of phytoplankton and bacterioplankton in hypertrophic shallow lakes

The aim of this work was to assess the temporal patterns in the community composition of phytoplankton (PCC) and bacterioplankton (BCC) in two interconnected and hypertrophic Pampean shallow lakes in Argentina. Factors shaping their community dynamics and community temporal covariations were also analysed. We performed 4 years of seasonal samplings (2012-2016) and communities were studied by the Utermöhl approach (PCC) and Illumina MiSeq sequencing (BCC). We found marked seasonal variations in both communities and inter-annual variations with decreasing microbial community similarities during the study. We also observed covariation in community-level dynamics among PCC and BCC within and between shallow lakes. The within-lake covariations remained positive and significant, while controlling for the effects of intrinsic (environmental) and extrinsic (temporal and meteorological) factors, suggesting a community coupling mediated by intrinsic biotic interactions. Algal-bacterial associations between different taxa of phytoplankton and bacterioplankton within each lake were also found. PCC was mainly explained by pure regional extrinsic (17-21%) and intrinsic environmental (8-9%) factors, while BCC was explained by environmental (8-10%) and biotic interactions with phytoplankton (7-8%). Our results reveal that the influence of extrinsic regional factors can be channeled to bacterioplankton through both environmental (i.e. water temperature) and phytoplankton effects.

Comparison of Prokaryotic Communities Associated with Different TOC Concentrations in Dianchi Lake

The effect of total organic carbon (TOC) on the prokaryotic community structure in situ has been rarely known. This study aimed to determine the effect of TOC level on the composition and networks of archaeal and bacterial communities in the sediments of Dianchi Lake, one of the most eutrophic lakes in China. Microbial assemblages showed significantly associations with TOC. Moreover, relatively high and low TOC formed taxonomic differences in prokaryotic assemblages. According to the results, the most abundant bacteria across all samples were identified as members of the phyla Proteobacteria, Nitrospirae, Chloroflexi, Firmicutes and Ignavibacteriae. The dominant groups of archaea consisted of Euryarchaeota, Woesearchaeota DHVEG-6, Bathyarchaeota and WSA2. Lastly, the meta-analysis results highlighted that the low TOC (LT) prokaryotic community structure is larger and more complex compared to moderate TOC (MT). On the whole, the prokaryotic community structure is obviously distinct among groups with different TOC levels, and LT communities may interact with each other strongly in the Dianchi Lake sediment. This study can provide more insights into prokaryotic assemblages in eutrophic lake sediment and provide suggestions for the restoration and maintenance of sediment ecosystems.