Assembly of a Benthic Microbial Community in a Eutrophic Bay with a Long History of Oyster Culturing

The introduction of oysters to a waterbody is an efficient method for decreasing levels of eutrophication. Oysters affect sedimental environments and benthic microbes via their roles in nutrient cycling. However, little is known about how long-term oyster culturing affects benthic microbial community assembly. In the present study, top and bottom sediments from an oyster-culture area and non-culture area, in a eutrophic bay with a long history of oyster culturing, were obtained for environmental parameter measurement and microbe identification. Deterministic and stochastic processes in microbial community assembly were assessed. In particular, keystone species identification through network analysis was combined with measured environmental parameters to determine the factors related to community assembly processes. Our results suggest that oyster culturing relates to greater variation in both biological and non-biological sediment profiles. In benthic communities, Proteobacteria and Chloroflexi were the most abundant phyla, and community compositions were significantly different between sample groups. We also found that community assembly was more affected by deterministic factors than stochastic ones, when oysters were present. Moisture, or water content, and pH were identified as affecting deterministic and stochastic processes, respectively, but only water content was a driver associated with oyster culturing. Additionally, although keystone species presented a similar pattern of composition to peripheral species, they responded to their environments differently. Furthermore, model selection, fitting keystone species to community assembly processes, indicates their role in shaping microbial communities.

Planktonic and Benthic Bacterial Communities of the Largest Central European Shallow Lake, Lake Balaton and Its Main Inflow Zala River

Lake Balaton is the largest European shallow lake, which underwent cultural eutrophication in the ‘70–80s. Therefore, strict pollution control measures were introduced and the water quality has become meso-eutrophic since the millennium. Due to the touristic significance and change in trophic levels of the lake, numerous ecological studies were carried out, but none of them was focused on both benthic and planktonic microbial communities at the same time. In our study, an attempt was made to reveal the spatial bacterial heterogeneity of the Lake Balaton and Zala River by 16S rDNA terminal restriction fragment length polymorphism fingerprinting and Illumina amplicon sequencing methods in the summer of 2017. According to the molecular biology results, mostly well-known freshwater microorganisms, adapted to nutrient-poor conditions were found in the pelagic water column. The LD12 subclade member Fonsibacter ubiquis, the cyanobacterial Synechococcus sp. and unknown Verrucomicrobia species were abundant in the less nutrient-dense basins, while the hgcI clade members showed various distribution. In the estuary and in the nutrient-dense western part of the lake, some eutrophic conditions preferring cyanobacteria (filamentous Anabaena and Aphanizomenon species) were also detectable. The benthic microbial community showed higher diversity, according to the observed appearance of microorganisms adapted to the deeper, less aerated layers (e.g. members of Desulfobacteraceae, Nitrosomonadaceae).

Impact of deep-sea polymetallic nodule mining on benthic microbial community and mediated biogeochemical functions

<p>Industrial-scale mining of deep-sea polymetallic nodules will remove nodules in large areas and impact the physical integrity of the seafloor. However, environmental standards for seafloor integrity and studies of recovery from environmental impacts are still largely missing. Further we have only a poor understanding of the role of nodules in shaping benthic microbial diversity and element cycles. We revisited the deep-sea disturbance and recolonization experiment carried out with a towed plough harrow in 1989 in the Peru Basin nodule field within a circular area of approx. 3.5 km diameter (>4100 m water depth). In the experimental area, the 26 years old plough tracks were still visible and showed different types and levels of disturbance such as removal and compaction of surface sediments. Microbial communities and their diversity were studied in disturbance tracks and undisturbed sites and related to habitat integrity, remineralization rates, and carbon flow. Locally, microbial activity was reduced up to 4 times in the impacted areas. Microbial cell numbers were reduced by ~50% in fresh, and by <30% in the old tracks. Our data suggest that microbially-mediated biogeochemical functions need more than 50 years to return to undisturbed levels in the sediments. In areas with nodules (i.e., outside the disturbance tracks) microbial communities in the nodules themselves were studied. Nodule communities were distinct from sediments and showed a lower diversity and a higher proportion of sequences related to potential metal-cycling bacteria (i.e. Magnetospiraceae, Hyphomicrobiaceae), bacterial and archaeal nitrifiers (i.e. <em>AqS1</em>, unclassified Nitrosomonadaceae, <em>Nitrosopumilus</em>, <em>Nitrospina</em>, <em>Nitrospira</em>), as well as bacterial sequences typically found in ocean crust, hydrothermal deposits and sessile fauna. Our results confirm that nodules host specific microbial communities with potentially significant contributions to organic carbon remineralization and metal cycling. This study contributes to developing environmental standards for deep-sea mining and highlights the limits for maintaining and recovering ecological integrity and functions during large-scale nodule mining.</p>

Response of sedimentary processes to cyanobacteria loading

<p>Sedimentation of pelagic cyanobacteria in dystrophic freshwater and oligohaline lagoons results in large inputs of labile organic matter (OM) to the benthos. We used an experimental approach to study the short-term impact of such phenomena on the benthic microbial community metabolism and on the nitrogen (N) fluxes across the sediment-water interface. We hypothesized an increase of respiratory activity, including N loss via denitrification and its recycling to the water column. Our results show that the incorporation within sediments of the settled bloom increases benthic bacterial activities. This is coupled to large DON and NH₄⁺ effluxes, and to a comparatively smaller increase of N₂ production, while no significant effects were detected for the benthic fluxes of NO_x^-. We constructed flow schemes for N compounds, which show that while denitrification was significantly stimulated by amending cyanobacterial biomass to the sediments, it represented less than 1% of total OM mineralization. Interestingly, we observed that total released nitrogen (DIN+DON+N₂ efflux) was dominated by DON, which contributed 75–80 % of the net N efflux, suggesting incomplete mineralization of OM. With the measured total N mobilization rate of about 15 mmol N m^-2 d^-1 it would take more than 4 months to regenerate the total organic N input to sediments (2031 mmol N m^-2), which represents the post-bloom deposited particulate organic N. These results suggest limited losses to the atmosphere and slow diffusive recycling of N buried into sediments, mostly as DON. Such regenerated N may eventually be flushed to the open sea or sustain pelagic blooms within the estuarine environment, including cyanobacteria, with a negative feedback for further import of atmospheric nitrogen via N-fixation.</p>