Microbial assembly, interaction, functioning, activity and diversification: a review derived from community compositional data

Abstract

Microorganisms play crucial roles in maintaining ecosystem stability. The last two decades have witnessed an upsurge in studies on marine microbial community composition using high-throughput sequencing methods. Extensive mining of the compositional data has provided exciting new insights into marine microbial ecology from a number of perspectives. Both deterministic and stochastic processes contribute to microbial community assembly but their relative importance in structuring subcommunities, that are categorized by traits such as abundance, functional type and activity, differs. Through correlation-based network analysis, significant progress has been made in unraveling microbial co-occurrence patterns and dynamics in response to environmental changes. Prediction of ecosystem functioning, based on microbial data, is receiving increasing attention, as closely related microbes often share similar ecological traits and microbial diversity often exhibits significant correlations to ecosystem functioning. The ecosystem functioning is likely executed not by the whole community, but rather by an active fraction of a community, which can be inferred from the marker gene transcription level of community members. Furthermore, the huge amount of microbial community data has significantly expanded the tree of life and illuminated microbial phylogenetic divergence and evolutionary history. This review summarizes important findings in microbial assembly, interaction, functioning, activity and diversification, highlighting the interacting roles of different aspects, derived from community compositional data.

Seasonal Niche Partitioning of Surface Temperate Open Ocean Prokaryotic Communities

“…Correlation-based network-analysis ( Liu et al, 2019 ) is receiving increased attention as a tool to advance our knowledge of connectivity between microbial taxa. Studies based on operational taxonomic units (OTUs) have revealed seasonal cycles and co-occurrence patterns among ammonia-oxidizing archaea, SAR11, SAR86, Cyanobacteria, Actinobacteria, and Flavobacteria microbial OTUs and other common groups ( Beman et al, 2011 ; Chow et al, 2013 ), outlining potential ecological networks.…”

Metagenomic and Metaproteomic Insights into Photoautotrophic and Heterotrophic Interactions in a Synechococcus Culture

“…I nteractions between photoautotrophic and heterotrophic bacteria shape the structure and diversity of upper ocean ecosystems and are foundational to marine food webs (1)(2)(3). Phytoplankton are significant contributors to primary production in aquatic environments, and marine picocyanobacteria primarily comprising Prochlorococcus and Synechococcus species account for almost half of the total ocean primary production (4,5).…”

Environmental Factors and Pollution Stresses Select Bacterial Populations in Association With Protists

“…The Pseudoalteromonas phylotypes were consistently present in the DRB assemblages under the conditions having a photic period, probably contributing to anti-fungal infection by more actively producing antifungal polyketide alteramides during the dark period (Moree et al, 2014). Thus, the co-occurrence of these two bacterial taxa may be of benefit to the host for a balance between rapid growth and low pathogenic infection under a natural diel light-dark condition (Liu et al, 2019). Gomiero and Viarengo (2014) showed that the antibiotic OTC (3.2 µM to 32 mM) treatments induced changes in the growth, survival, endocytosis rate, and lysosomal membrane stability of the marine ciliate Euplotes crassus.…”