Free‐living and particle‐associated microbial communities play critical roles in nutrient cycles in aquatic systems. However, little is known about their assembly process, function, and interactions. Here, by using 16S rRNA gene amplicon sequencing of size‐fractionated samples collected during the wet and dry seasons, we investigated the assembly processes and co‐occurrence patterns of bacterial and archaeal communities in the Shenzhen River‐Bay system, South China. The bacterial and archaeal communities showed specific distribution patterns according to the size fraction (free‐living vs. particle‐associated), habitat (river vs. estuary), and seasonality (wet vs. dry season). Neutral modeling revealed that the stochastic pattern was more pronounced for bacteria than archaea, although both deterministic and stochastic processes significantly influenced the assembly of bacterial and archaeal communities. Homogeneous selection had a relatively higher importance in structuring bacterioplankton in free‐living fractions, while this process was more important in structuring archaeaplankton in particle‐associated fractions. Aquatic microbial community composition and assembly processes were most strongly associated with salinity and water temperature. Network analysis for each size fraction of the plankton revealed higher connectivity in the particle‐associated communities than the free‐living communities for intra‐bacteria, inter‐bacteria/archaea, and intra‐archaea associations, accordingly, when nonlinear associations were considered. These findings expand the current understanding of the ecological mechanisms and Archaea‐Bacteria interactions, underlying the size‐fractionated plankton dynamics in the river‐bay system.

Fungi are key components of microbial community in mangrove wetlands, with important roles in the transformation of nutrients and energy. However, existing studies typically focus on cultivable fungi, and seldomly on the structure and driving factors of the entire fungal communities. The compositions, community assembly and interaction patterns of mangrove fungal community on large scale remain elusive. Here, biogeography, assembly and co-occurrence patterns of fungal communities in mangrove across Eastern to Southern China were systematically analyzed by targeting the entire ITS region with high-throughput Pacific Biosciences single-molecule real-time sequencing. The analysis recovered a high level of fungal diversity, including a number of basal fungal lineages not previously reported in mangroves, such as Rozellomycota and Chytridiomycota . Beta nearest-taxon index analyses suggested a determinant role of dispersal limitation on fungal community in overall and most individual mangroves, with supporting from the strong distance-decay patterns of community similarity. Further, nonmetric multidimensional scaling analyses revealed a similar biogeography of dominant and rare fungal community. A minor role of environmental selection on the fungal community was noted, with geographical location and sediment depth as crucial factors driving the distribution of both, the dominant and rare taxa. Finally, network analysis revealed high modularized co-occurrence patterns of fungal community in mangrove sediments, and the keystone taxa might play important roles in microbial interactions and ecological functions. The investigation expands our understanding of biogeography, assembly patterns, driving factors, and co-occurrence relationships of mangrove fungi, and will spur the further functional exploration and protection of fungal resources in mangrove. IMPORTANCE As key components of microbial community in mangroves, fungi have important ecological functions. However, fungal community in mangrove on large scale is generally elusive, and mangroves are declining rapidly due to climate change and anthropogenic activities. This work provided an overview of fungal community structure and biogeography in mangrove wetlands along an over-9000 km coastline across Eastern to Southern China. Our study observed a high number of basal fungal lineages in mangrove sediments, such as Rozellomycota and Chytridiomycota . In addition, our results highlighted a crucial role of dispersal limitation and a minor role of environmental selections on fungal community in mangrove sediments. These novel findings add important knowledge about the structure, assembly processes, and driving factors of fungal community in mangrove sediments.

As a key microbial community component with important ecological roles, archaea merit the attention of biologists and ecologists. The mechanisms controlling microbial community diversity, composition, and biogeography are central to microbial ecology but poorly understood.

Due to the high divergence among 16S rRNA genes of anammox bacteria, different diversity pattern of the community could be resulted from using different primer set. In this study, the efficiencies and specificities of two commonly used sets, Amx368F/Amx820R and Brod541F/Amx820R, were evaluated by exploring the diversity characteristics of anammox bacteria in sediments from marine, estuary, and freshwater wetland. Statistical analysis indicated that the base mispairing rate between bases on 16S rRNA gene sequences retrieved by Amx368F/Amx820R and their corresponding ones on primer Brod541F was quite high, suggesting the different efficiency and specificity of Amx368F/Amx820R and Brod541F/Amx820R. Further experimental results demonstrated that multiple genera of anammox bacteria, including Ca. Scalindua, Ca. Brocadia, and Ca. Kuenenia, were able to be detected by Amx368F/Amx820R, but only Ca. Scalindua could be retrieved by Brod541F/Amx820R. Moreover, the phylogenetic clusters of Ca. Scalindua by Amx368F/Amx820R were different completely from those by Brod541F/Amx820R, presenting a significant complementary effect. By joint application of these two primer sets, the diversity distribution patterns of anammox bacteria in different environments were analyzed. Almost all retrieved sequences from marine sediments belonged to Ca. Scalindua. Sequences from freshwater wetland were affiliated to Ca. Brocadia and two new clusters, while high diversity of anammox bacteria was found in estuary, including Ca. Scalindua, Ca. Brocadia, and Ca. Kuenenia, corresponding to the river-sea intersection environmental feature. In total, these two prime sets have different characteristic for anammox bacteria detecting from environmental samples, and their combined application could achieve better diversity display of anammox community.

Background: Mangrove wetlands are unique ecosystems with specific environmental characteristics, and are a hotspot of biodiversity. Although they probably harbor a variety of mangrove-specific fungi, the compositions of mangrove fungal community has been rarely investigated in detail, except for few published culture-based studies. In addition, the fungal community assembly and interaction patterns that impact the community composition in mangroves have not been explored to date. Results: We used the Pacific Biosciences single-molecule real-time sequencing approach targeting the entire internal transcribed spacer region, to systematically investigate the composition, biogeographical patterns, assembly processes, co-occurrence patterns and shaping factors of the fungal communities in sediments of seven representative mangroves across the Southeast China. We recovered 15 phyla, including some early diverging fungal lineages not previously reported in mangroves. Phylogenetic analysis revealed an incredibly high proportion of Rozellomycota and Chytridiomycota, as accounting for up to one-third of all fungal abundance. Although the neutral community model described a moderate portion of community variation, the similarity of fungal communities exhibited strong distance-decay patterns. Furthermore, the mean values and most beta nearest-taxon index fell between -2 to 2, with Bray–Curtis-based Raup–Crick value generally greater than 0.95, suggesting that stochastic processes strongly shape the fungal community composition. Consistently, nonmetric multidimensional scaling and permutational multivariate analysis of variance confirmed the geographical location as a crucial factor driving the distribution of both, the dominant and rare taxa of mangrove fungi. The db-RDA analyses indicated a minor role of environmental selections in shaping the fungal community. Network analyses revealed that the deep sediments harbor more complex fungal networks with highly connected taxa than surface sediments, and that rare fungal taxa might play important roles in microbial interactions and ecological functions in mangrove sediments.Conclusions: The investigation revealed high fungal diversity in mangrove sediments, with incredibly high numbers of basal fungal lineages, stochastic processes driving the assembly of fungal community, and geographic location strongly shaping fungal community composition in mangroves. These discoveries therefore spur further studies of the utilization and protection of fungal resources and communities in mangrove sediments.