Conservation of Species- and Trait-Based Modeling Network Interactions in Extremely Acidic Microbial Community Assembly

Malonic acid shapes bacterial community dynamics in compost to promote carbon sequestration and humic substance synthesis

The incorporation of malonic acid (MA) into compost as a regulator of the tricarboxylic acid (TCA) cycle has the potential to increase carbon sequestration. However, the influence of MA on the transformation of the microbial community during the composting process remains unclear. In this investigation, MA was introduced at different stages of chicken manure (CM) composting to characterize the bacterial community within the compost using high-throughput sequencing. We assess the extent of increased carbon sequestration by comparing the concentration of total organic carbon (TOC). At the same time, this study examines whether increased carbon sequestration contributes to humus formation, which was elucidated by evaluating the content and composition of humus. Our results show that the addition of MA significantly improved carbon sequestration within the compost, reducing the carbon loss rate (C loss (%)) from 64.70% to 52.94%, while increasing HS content and stability. High throughput sequencing and Random Forest (RF) analysis show that the introduction of MA leads to a reduction in the diversity of the bacterial communities, but enhanced the ability of bacterial communities to synthesize humus. Furthermore, the addition of MA favors the proliferation of Firmicutes. Also, the hub of operational taxonomic units (OTUs) within the community co-occurrence network shifts from Proteobacteria to Firmicutes. Remarkably, our study finds a significant decrease in negative correlations between bacteria, potentially mitigating substrate consumption due to negative interactions such as competition. This phenomenon contributes to the improved retention of TOC in the compost. This research provides new insights into the mechanisms by which MA regulates bacterial communities in compost, and provides a valuable theoretical basis for the adoption of this innovative composting strategy.

Vertical environmental gradient drives prokaryotic microbial community assembly and species coexistence in a stratified acid mine drainage lake

Acid mine drainage (AMD) lakes are typical hydrologic features caused by open pit mining and represent extreme ecosystems and environmental challenges. Little is known about microbial distribution and community assembly in AMD lakes, especially in deep layers. Here, we investigated prokaryotic microbial diversity and community assembly along a depth profile in a stratified AMD lake using 16S rRNA gene sequencing combined with multivariate ecological and statistical methods. The water column in the AMD lake exhibited tight geochemical gradients, with more acidic surface water. Coupled with vertical hydrochemical variations, prokaryotic microbial community structure changed significantly, and was accompanied by increased diversity with depth. In the surface water, heterogeneous selection was the most important assembly process, whereas stochastic processes gained importance with depth. Meanwhile, microbial co-occurrences, especially positive interactions, were more frequent in the stressful surface water with reduced network modularity and keystone taxa. The pH was identified as the key driver of microbial diversity and community assembly along the vertical profile based on random forest analysis. Taken together, environmental effects dominated by acid stress drove the community assembly and species coexistence that underpinned the spatial scaling patterns of AMD microbiota in the lake. These findings demonstrate the distinct heterogeneity of local prokaryotic microbial community in AMD lake, and provide new insights into the mechanism to maintain microbial diversity in extreme acidic environments.

Bacterial Communities Present Distinct Co-occurrence Networks in Sediment and Water of the Thermokarst Lakes in the Yellow River Source Area

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.

Temperature and microbial interactions drive the deterministic assembly processes in sediments of hot springs

Terrestrial geothermal ecosystems, as a representative of extreme environments, exhibit a variety of geochemical gradients, and their microbes are thought to be under high stress through environmental selection. However, it is still unclear how stochasticity and biotic interactions contribute to the microbial community assembly in hot springs. Here, we investigated the assembly processes and co-occurrence patterns of microbiota (i.e. bacteria and archaea) in both water and sediments sampled from fifteen hot springs in the Tengchong area, Southwestern of China, using 16S rRNA gene sequencing combined with multivariate ecological and statistical methods. These hot springs harbored more specialists than non-geothermal ecosystems, which are well-adapted to the extreme conditions, as shown by extremely high nearest-taxon index (NTI) and narrower niche width. Habitat differentiation led to the differences in microbial diversity, species-interactions, and community assembly between water and sediment communities. The sediment community showed stronger phylogenetic clustering and was primarily governed by heterogeneous selection, while undominated stochastic processes and dispersal limitation were the major assembly processes in the water community. Temperature and ferrous iron were the major factors mediating the balance of stochastic and deterministic assembly processes in sediment communities, as evidenced by how divergences in temperature and ferrous iron increased the proportion of determinism. Microbial interactions in sediments contributed to deterministic community assembly, as indicated by more complex associations and greater responsiveness to environmental change than water community. These findings uncover the ecological processes underlying microbial communities in hot springs, and provide potential insight into understanding the mechanism to maintain microbial diversity in extreme biospheres.

Bacterial Communities in Stream Biofilms in a Degrading Grassland Watershed on the Qinghai-Tibet Plateau

Grassland is among the largest terrestrial biomes and is experiencing serious degradation, especially on the Qinghai-Tibet Plateau (QTP). However, the influences of grassland degradation on microbial communities in stream biofilms are largely unknown. Using 16S rRNA gene sequencing, we investigated the bacterial communities in stream biofilms in sub-basins with different grassland status in the Qinghai Lake watershed. Grassland status in the sub-basins was quantified using the normalized difference vegetation index (NDVI). Proteobacteria, Bacteroidetes, Cyanobacteria, and Verrucomicrobia were the dominant bacterial phyla. OTUs, 7,050, were detected in total, within which 19 were abundant taxa, and 6,922 were rare taxa. Chao 1, the number of observed OTUs, and phylogenetic diversity had positive correlations with carbon (C), nitrogen (N), and/or phosphorus (P) in biofilms per se. The variation of bacterial communities in stream biofilms was closely associated with the rate of change in NDVI, pH, conductivity, as well as C, N, P, contents and C:N ratio of the biofilms. Abundant subcommunities were more influenced by environmental variables relative to the whole community and to rare subcommunities. These results suggest that the history of grassland degradation (indicated as the rate of change in NDVI) influences bacterial communities in stream biofilms. Moreover, the bacterial community network showed high modularity with five major modules (>50 nodes) that responded differently to environmental variables. According to the module structure, only one module connector and 12 module hubs were identified, suggesting high fragmentation of the network and considerable independence of the modules. Most of the keystone taxa were rare taxa, consistent with fragmentation of the network and with adverse consequences for bacterial community integrity and function in the biofilms. By documenting the properties of bacterial communities in stream biofilms in a degrading grassland watershed, our study adds to our knowledge of the potential influences of grassland degradation on aquatic ecosystems.

Nutrients Drive the Structures of Bacterial Communities in Sediments and Surface Waters in the River-Lake System of Poyang Lake

Lake and its inflow rivers compose a highly linked river-lake system, within which sediment and water are also closely connected. However, our understanding of this linked and interactive system remains unclear. In this study, we examined bacterial communities in the sediments and surface waters in Poyang Lake and its five tributaries. Bacterial communities were determined while using high-throughput 16S rRNA gene sequencing. The results showed significant differences of bacterial communities between sediments and surface waters, as well as between Poyang lake and its tributaries, suggesting that the river-lake system of Poyang Lake provides diverse and distinct habitats for bacterial communities, including lake water, lake sediment, river water, and river sediment. These biomes harbor distinct bacterial assemblages. Sediments harbor more diverse bacterial taxa than surface waters, but the bacterial communities in surface waters were more different across this river-lake system than those in sediments. In this eutrophic river-lake ecosystem, nitrogen and phosphorus were important drivers in sediment bacterial communities. Nitrogen, phosphorus, and dissolved organic carbon, as well as their stoichiometric ratios affected bacterial communities in surface waters. Moreover, network analysis revealed that the bacterial communities in surface waters were more vulnerable to various disturbances than in sediments, due to lower alpha diversity, high complexity of network, and a small number of key taxa (module hubs and connectors). Nutrient variables had strong influences on individual operational taxonomic units (OTUs) in the network, especially in bacterial network in surface waters. Different groups of taxa responded differently to nutrients, with some modules being more susceptible to nutrient variations. This study increased our current knowledge of linked river-lake ecosystems and provided valuable understanding for effective management and protection of these ecosystems by revealing bacterial communities in sediments and surface waters in Poyang Lake and its tributaries, as well as their responses to nutrients variation.

Taxonomic and Functional Differences between Microbial Communities in Qinghai Lake and Its Input Streams

Understanding microbial communities in terms of taxon and function is essential to decipher the biogeochemical cycling in aquatic ecosystems. Lakes and their input streams are highly linked. However, the differences between microbial assemblages in streams and lakes are still unclear. In this study, we conducted an intensive field sampling of microbial communities from lake water and stream biofilms in the Qinghai Lake watershed, the largest lake in China. We determined bacterial communities using high-throughput 16S rRNA gene sequencing and predicted functional profiles using PICRUSt to determine the taxonomic and functional differences between microbial communities in stream biofilms and lake water. The results showed that stream biofilms and lake water harbored distinct microbial communities. The microbial communities were different taxonomically and functionally between stream and lake. Moreover, streams biofilms had a microbial network with higher connectivity and modularity than lake water. Functional beta diversity was strongly correlated with taxonomic beta diversity in both the stream and lake microbial communities. Lake microbial assemblages displayed greater predicted metabolic potentials of many metabolism pathways while the microbial assemblages in stream biofilms were more abundant in xenobiotic biodegradation and metabolism and lipid metabolism. Furthermore, lake microbial assemblages had stronger predicted metabolic potentials in amino acid metabolism, carbon fixation, and photosynthesis while stream microbial assemblages were higher in carbohydrate metabolism, oxidative phosphorylation, and nitrogen metabolism. This study adds to our knowledge of stream-lake linkages from the functional and taxonomic composition of microbial assemblages.