Vertical partitioning of freshwater bacterioplankton community in a deep mesotrophic lake with a fully oxygenated hypolimnion (Lake Biwa, Japan)

Abstract

In freshwater microbial ecology, extensive studies are attempting to characterize the vast majority of uncultivated bacterioplankton taxa. However, these studies mainly focus on the epilimnion and little is known regarding the bacterioplankton inhabiting the hypolimnion of deep holomictic lakes, despite its biogeochemical importance. In this study, we investigated the bacterioplankton community composition in a deep freshwater lake with a fully oxygenated hypolimnion (Lake Biwa, Japan) using high-throughput 16S rRNA gene amplicon sequencing. Sampling at a pelagic site over 15 months throughout the water column revealed that the community composition in the hypolimnion was significantly different from that in the epilimnion. The bacterial community in the hypolimnion was composed of groups dominating in the whole water layer (e.g., bacI-A1 and acI-B1) and groups that were hypolimnion habitat specialists. Among the hypolimnion specialists, members of Chloroflexi and Planctomycetes were highly represented (e.g., CL500-11, CL500-15 and CL500-37), followed by members of Acidobacteria, Chlorobi and nitrifiers (e.g., Ca. Nitrosoarchaeum, Nitrosospira and Nitrospira). This study identified the number of previously understudied taxa dominating the deep aerobic freshwater habitat, suggesting that the biogeochemical cycling there is driven by the microbial community that are different from that in the epilimnion.

Genome‐resolved viral and cellular metagenomes revealed potential key virus‐host interactions in a deep freshwater lake

“…The second shift in the virion community from December to January likely resulted from the onset of winter vertical mixing (Supporting Information Table S1), which intermingled the epilimnetic and hypolimnetic viral communities, as observed for bacterioplankton (Okazaki et al ., , ; Okazaki and Nakano, ). Alternatively, environmental stresses associated with the mixing event (e.g., increased solar radiation) could have induced lysogens in the lytic cycle (Winter et al ., ) and resulted in the observed viral community shift.…”

“…). The depth‐stratified viral community is analogous to that reported from ocean (Hurwitz et al ., ; Mizuno et al ., ; Paez‐Espino et al ., ; López‐Pérez et al ., ; Luo et al ., ) and likely reflects the depth‐stratified community of bacterioplankton (Okazaki and Nakano, ) (Supporting Information Table S4).…”

“…Induction can also be trigged by the increasing cell abundance or improved physiological condition of the host, with the virus acting as a ‘time bomb’ and breaking the symbiotic relationship with their host once the host has successfully bloomed in the environment (Paul, ; Brum et al ., ). Indeed, hypolimnion‐specific bacterial lineages often take months to archive their peak abundance (Okazaki et al ., ; ; Okazaki and Nakano, ), suggesting that lysogeny (or presudolysogeny) is preferred strategy for viruses during the long growth phase of the host. No difference in cellular‐virion preference ( P cell ) was observed between water layers (Supporting Information Fig.…”

“…Levybacteria (OP11) and Ca. Saccharibacteria (TM7) (Brown et al, 2015), had not been reported in a previous study conducted at Lake Biwa using 16S rRNA gene amplicon sequencing (Okazaki and Nakano, 2016), as these phyla harbour 16S rRNA gene sequences that are undetectable with conventional universal primers.…”

Competition and niche separation of pelagic bacteria in freshwater habitats

“…Such processes might in fact translate the patchiness of substrate concentrations that is biologically generated at a micro‐ and mesoscale into larger, eventually system‐wide patterns of heterogeneity (Horňák et al ., ). The most obvious spatial pattern in deep, thermally stratified lakes is a clear distinction between the microbial assemblages in the oxygenated epi‐ and hypolimnetic realms (Okazaki et al ., ; Okazaki and Nakano, ): Various groups of photoheterotrophic bacteria featuring light‐harvesting pigments are typical for the upper, photic zone (Atamna‐Ismaeel et al ., ; Sharma et al ., ; Martinez‐Garcia et al ., ), whereas the deeper zones harbour microbial taxa with distinct physiological traits that are rare or absent in the surface layers, such as Chloroflexi (Denef et al ., ), Thaumarchaeota (Callieri et al ., ; Berdjeb et al ., ; Coci et al ., ) or methylotrophs (Salcher et al ., ).…”