Bottom–up selection has an important role in microbial community assembly but is unable to account for all observed variance. Other processes like top–down selection (e.g., predation) may be partially responsible for the unexplained variance. However, top–down processes and their interaction with bottom–up selective pressures often remain unexplored. We utilised an in situ marine biofilm model system to test the effects of bottom–up (i.e., substrate properties) and top–down (i.e., large predator exclusion via 100 µm mesh) selective pressures on community assembly over time (56 days). Prokaryotic and eukaryotic community compositions were monitored using 16 S and 18 S rRNA gene amplicon sequencing. Higher compositional variance was explained by growth substrate in early successional stages, but as biofilms mature, top–down predation becomes progressively more important. Wooden substrates promoted heterotrophic growth, whereas inert substrates’ (i.e., plastic, glass, tile) lack of degradable material selected for autotrophs. Early wood communities contained more mixotrophs and heterotrophs (e.g., the total abundance of Proteobacteria and Euglenozoa was 34% and 41% greater within wood compared to inert substrates). Inert substrates instead showed twice the autotrophic abundance (e.g., cyanobacteria and ochrophyta made up 37% and 10% more of the total abundance within inert substrates than in wood). Late native (non-enclosed) communities were mostly dominated by autotrophs across all substrates, whereas high heterotrophic abundance characterised enclosed communities. Late communities were primarily under top–down control, where large predators successively pruned heterotrophs. Integrating a top–down control increased explainable variance by 7–52%, leading to increased understanding of the underlying ecological processes guiding multitrophic community assembly and successional dynamics.

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Microbial rhodopsins are simple light-harvesting complexes that, unlike chlorophyll photosystems, have no iron requirements for their synthesis and phototrophic functions. Here, we report the environmental concentrations of rhodopsin along the Subtropical Frontal Zone off New Zealand, where Subtropical waters encounter the iron-limited Subantarctic High Nutrient Low Chlorophyll (HNLC) region. Rhodopsin concentrations were highest in HNLC waters where chlorophyll-a concentrations were lowest. Furthermore, while the ratio of rhodopsin to chlorophyll-a photosystems was on average 20 along the transect, this ratio increased to over 60 in HNLC waters. We further show that microbial rhodopsins are abundant in both picoplankton (0.2-3 μm) and in the larger (>3 μm) size fractions of the microbial community containing eukaryotic plankton and/or particle-attached prokaryotes. These findings suggest that rhodopsin phototrophy could be critical for microbial plankton to adapt to resource-limiting environments where photosynthesis and possibly cellular respiration are impaired.

Sinking organic particles from surface waters provide key nutrients to the deep ocean, and could serve as vectors transporting microbial diversity to the deep ocean. However, the effect of this seasonally varying connectivity with the surface on deep microbial communities remains unexplored. Here, a three-year time-series from surface and deep (500 m) waters part of the Munida Microbial Observatory Time-Series (MOTS) was used to study the seasonality of epipelagic and mesopelagic prokaryotic communities. The goal was to establish how seasonally dynamic these two communities are, and any potential linkages between them. Both surface and deep prokaryotic communities displayed seasonality with high variation in community diversity. Deep prokaryotic communities mirrored the seasonal patterns in heterotrophic production and bacterial abundance displayed by surface communities, which were related to changes in chlorophyll-a concentration. However, the magnitude of this temporal variability in deeper waters was generally smaller than in the surface. Detection of surface prokaryotes in the deep ocean seemed seasonally linked to phytoplankton blooms, but other copiotrophic or typically algal-associated surface groups were not detected in the mesopelagic suggesting only specific populations were surviving the migration down the water column. We show transfer of organisms across depths is possibly not always unidirectional, with typically deep ocean microbes being seasonally abundant in surface waters. This indicates the main mechanism linking surface and deep communities changes seasonally: sinking of organic particles during productive periods, and vertical convection during winter overturning.

Marine microbes use extracellular phosphatases to hydrolyze phosphate from organic matter. Dissolved organic phosphorus (DOP) is typically present in higher concentrations than phosphate in oceanic surface waters. Yet, the fate and role of different DOP components, such as phosphomonoester and phosphodiester, are poorly understood. Most of the investigations on extracellular enzymatic hydrolysis of marine DOP have focused on phosphomonoesterase (MEA) activity (i.e., alkaline phosphatase), whereas phosphodiesterase (DEA) measurements are scarce. This limits our understanding of the ecological and biogeochemical role of DOP sources other than P-monoesters in the sea. We determined extracellular MEA and DEA activities including their cell-free fractions on a bimonthly basis over 14 months in surface and mesopelagic subantarctic waters, thus covering a wide range of phosphate availability levels (from <0.5 to 2.3 µM). We found that DEA and MEA exhibit similar hydrolysis rates in surface as well as in mesopelagic waters. The MEA:DEA ratio varied between 0.38 and 5.42 during the study period, indicating potential differences in function and/or expression among the two enzyme groups, potentially reflecting differences in the availability and/or utilization of P-monoester and P-diester pools. Interestingly, the MEA:DEA was negatively correlated to phosphate (r −0.82, p 0.02, R 2 0.67) and positively with the inorganic N:P ratio (r 0.84, p 0.02, R 2 0.67), suggesting that the relative importance of DEA vs. MEA is linked to inorganic P availability and the N:P ratio. DEA was also related to the N:P ratio, both at the surface and at depth, suggesting DEA alone is sensitive to changes in the N:P ratio. The majority (>70%) of extracellular MEA and DEA was found in the cell-free fraction, increasing with depth for MEA. Our results indicated that DOP hydrolysis mediated by DEA in the surface as well as in dark ocean is as important as the frequently measured MEA.