Bacterial Biogeography across the Amazon River-Ocean Continuum

Abstract

Spatial and temporal patterns in microbial biodiversity across the Amazon river-ocean continuum were investigated along ∼675 km of the lower Amazon River mainstem, in the Tapajós River tributary, and in the plume and coastal ocean during low and high river discharge using amplicon sequencing of 16S rRNA genes in whole water and size-fractionated samples (0.2–2.0 μm and >2.0 μm). River communities varied among tributaries, but mainstem communities were spatially homogeneous and tracked seasonal changes in river discharge and co-varying factors. Co-occurrence network analysis identified strongly interconnected river assemblages during high (May) and low (December) discharge periods, and weakly interconnected transitional assemblages in September, suggesting that this system supports two seasonal microbial communities linked to river discharge. In contrast, plume communities showed little seasonal differences and instead varied spatially tracking salinity. However, salinity explained only a small fraction of community variability, and plume communities in blooms of diatom-diazotroph assemblages were strikingly different than those in other high salinity plume samples. This suggests that while salinity physically structures plumes through buoyancy and mixing, the composition of plume-specific communities is controlled by other factors including nutrients, phytoplankton community composition, and dissolved organic matter chemistry. Co-occurrence networks identified interconnected assemblages associated with the highly productive low salinity near-shore region, diatom-diazotroph blooms, and the plume edge region, and weakly interconnected assemblages in high salinity regions. This suggests that the plume supports a transitional community influenced by immigration of ocean bacteria from the plume edge, and by species sorting as these communities adapt to local environmental conditions. Few studies have explored patterns of microbial diversity in tropical rivers and coastal oceans. Comparison of Amazon continuum microbial communities to those from temperate and arctic systems suggest that river discharge and salinity are master variables structuring a range of environmental conditions that control bacterial communities across the river-ocean continuum.

Patterns of Bacterial and Archaeal Gene Expression through the Lower Amazon River

“…Similar to findings by Doherty et al (2017) for microbial community composition, gene expression patterns detailed here are consistent with a spatially homogeneous mainstem in which microbial metabolism changes relatively little from Óbidos to the mouth in the well-mixed river, simultaneously supporting heterotrophic, chemoautotrophic, and photosynthetic processes. However, tributary inputs drive discrete communities with distinctive biogeochemical activities at Tapajós and Belém, and these are biased toward free-living cells that rely more on phototrophy.…”

“…Genes whose expression ratios were significantly predicted by these parameters encoded sulfur incorporation and oxidation, carbon storage, membrane biosynthesis, and carbon fixation in the free-living cells; and nitrogen and phosphorus acquisition, sulfur oxidation, and vitamin B6 biosynthesis in the particle-associated cells. These patterns echo an analysis of the taxonomic composition of the mainstem microbial communities in which spatially homogeneous assemblages were found in much of the lower reaches (Doherty et al, 2017) and analysis of the dissolved organic matter pool in which highly similar molecular composition was found within the mainstem (Seidel et al, 2016). The influence of the Amazon River and its resident microbes continues beyond the river boundaries.…”

“…River water constituents were determined as described in Ward et al (2013), Ward et al (2015), and Doherty et al (2017). Temperature and pH were measured using a Thermo Orion 290Aplus meter with the probe immersed in an overflowing graduated cylinder.…”

Flood pulse regulation of bacterioplankton community composition in an Amazonian floodplain lake

“…Synechococcus was amongst the most abundant genera in our study, being significantly overrepresented in communities during falling water. This genus also had high relative abundances in other AFLs (Toyama et al., ), but not in rivers (Doherty et al., ; Toyama et al., ). High temperatures and the food‐web structure of tropical aquatic environments enhance the contribution of these phototrophic picoplankton to primary production (Domingues et al., ; Sarmento, ).…”

“…Seasonal patterns in BCC are well documented in some temperate aquatic systems, where temperature appears to be the main force shaping BCC (Poretsky, Rodriguez-R, Luo, Tsementzi, & Konstantinidis, 2014;Rösel, Allgaier, & Grossart, 2012;Staley et al, 2015). However, few comparable studies have been carried out in tropical systems (Doherty et al, 2017;de Oliveira & Margis, 2015) so it remains unclear whether temperature is also the driving force there.…”