Cross-depth analysis of marine bacterial networks suggests downward propagation of temporal changes

Abstract

Interactions among microbes and stratification across depths are both believed to be important drivers of microbial communities, though little is known about how microbial associations differ between and across depths. We have monitored the free-living microbial community at the San Pedro Ocean Time-series station, monthly, for a decade, at five different depths: 5 m, the deep chlorophyll maximum layer, 150 m, 500 m and 890 m (just above the sea floor). Here, we introduce microbial association networks that combine data from multiple ocean depths to investigate both within-and between-depth relationships, sometimes time-lagged, among microbes and environmental parameters. The euphotic zone, deep chlorophyll maximum and 890 m depth each contain two negatively correlated 'modules' (groups of many inter-correlated bacteria and environmental conditions) suggesting regular transitions between two contrasting environmental states. Two-thirds of pairwise correlations of bacterial taxa between depths lagged such that changes in the abundance of deeper organisms followed changes in shallower organisms. Taken in conjunction with previous observations of seasonality at 890 m, these trends suggest that planktonic microbial communities throughout the water column are linked to environmental conditions and/or microbial communities in overlying waters. Poorly understood groups including Marine Group A, Nitrospina and AEGEAN-169 clades contained taxa that showed diverse association patterns, suggesting these groups contain multiple ecological species, each shaped by different factors, which we have started to delineate. These observations build upon previous work at this location, lending further credence to the hypothesis that sinking particles and vertically migrating animals transport materials that significantly shape the time-varying patterns of microbial community composition.

Habitat filtering of bacterioplankton communities above polymetallic nodule fields and sediments in the Clarion‐Clipperton zone of the Pacific Ocean

“…There can be substantial variation in diversity and function among individual bacterioplankton taxa at the phyla and class levels coupled with the dispersal capacity and response to environmental stressors of these taxa (see, e.g., Langenheder et al ., ; Comte et al ., ; Székely and Langenheder, ). Hence, while previous studies have highlighted the importance of environmental conditions in shaping the composition of entire microbial communities (see, e.g., Sunagawa et al ., ; Cram et al ., ; Salazar et al ., ), we extend these findings by inferring metacommunity assembly mechanisms from a well‐established theoretical framework and also to assess variation at the phyla and class level. Moreover, by applying a metacommunity framework to our analyses, we sought to characterize differential influences of spatial and environmental drivers on the assembly of bacterioplankton assemblages.…”

Keystone taxa predict compositional change in microbial communities

“…Under the assumption that cohesion measures biotic interactions (Herren and McMahon, 2017), our results support the hypothesis that biotic interactions are stabilizing to microbial community composition. Several recent studies have concluded that biotic interactions can be strong drivers of microbial population dynamics, on par with or exceeding the influence of environmental factors (Cram et al, 2015b;Cabello et al, 2016;Trivedi et al, 2017). For example, many marine bacterial taxa are more strongly related to other bacterial taxa than to habitat variables (Cram et al, 2015b).…”

Strong impact of anthropogenic contamination on the co‐occurrence patterns of a riverine microbial community

“…Due to advances in high‐throughput sequencing technologies, the increased availability of sequence data across large spatio‐temporal scales has provided an opportunity to address this gap in fundamental knowledge in microbial ecology. Recent studies have used co‐occurrence network analysis as a tool to decipher the potential intraspecies or interspecies interactions in the complex microbial assemblages in oceans (Cram et al ., ), lakes (Eiler et al ., ; Kara et al ., ) and soils (Barberan et al ., ; Berry and Widder, ; Ma et al ., ) as well as in anthropogenic environments such as activated sludge (Ju et al ., ), anaerobic digesters (Rui et al ., ) and the human gut (Faust et al ., ). These findings revealed that microbial communities generally have nonrandom co‐occurrence patterns and modular structures, which strongly implies the essential role of biotic interactions in governing community assembly and ecosystem function.…”