Linking Microbial Functioning and Trophic Pathways to Ecological Status in a Coastal Mediterranean Ecosystem

Coastal marine ecosystems host complex microbial communities whose composition and metabolism are influenced by continental inputs and mesoscale properties of seawater masses. The identifying traits of the phytoplankton and bacteria such as biomass, size, shape and their metabolism related to organic matter production and degradation, recognized as indicators of the functioning of an ecosystem, were observed in the Gulf of Manfredonia (South Adriatic Sea, Italy) in late spring. This Gulf area is characterized by terrestrial inputs and mesoscale circulation influence such as coastal waters flowing southward from the North Adriatic and offshore waters interested by the Ionian Sea. Water samples were grouped in clusters (Coastal, Intermediate, Offshore and Deep Systems) according to the water column properties. Phytoplankton community biomass and composition, autotrophic and total prokaryotic abundances and microbial metabolism such as enzyme activity rates and prokaryotic heterotrophic production were analyzed to elucidate the trophic pathways with the objective to infer on the ecosystem status. As expected, size-fractionated phytoplankton biomass and production showed greater concentration in coastal waters with prevalence of the largest fractions (micro- and nano-) supported by the diatoms. Conversely, lower biomass and production were measured in all off-shore waters, mainly sustained by smallest fractions (nano-sized phytoflagellates and picophytoplankton). Total and autotrophic prokaryotic abundance decreased from coastal to offshore stations, inversely with respect to cell volume. Prokaryotic heterotrophic production was just below 50% compared to that of phytoplankton in all waters, evidencing an active biomass synthesis. High alkaline phosphatase and leucine aminopeptidase in coastal and offshore waters suggested the quick regeneration of Phosphorus and protein decomposition, respectively. Different levels of phytoplankton-bacteria association might provide a tool to define the ecological status of the studied system in the observed period; an approach to ecosystem assessment exportable to other coastal systems is proposed.

Ocean Acidification Induces Changes in Virus–Host Relationships in Mediterranean Benthic Ecosystems

Acidified marine systems represent “natural laboratories”, which provide opportunities to investigate the impacts of ocean acidification on different living components, including microbes. Here, we compared the benthic microbial response in four naturally acidified sites within the Southern Tyrrhenian Sea characterized by different acidification sources (i.e., CO2 emissions at Ischia, mixed gases at Panarea and Basiluzzo and acidified freshwater from karst rocks at Presidiana) and pH values. We investigated prokaryotic abundance, activity and biodiversity, viral abundance and prokaryotic infections, along with the biochemical composition of the sediment organic matter. We found that, despite differences in local environmental dynamics, viral life strategies change in acidified conditions from mainly lytic to temperate lifestyles (e.g., chronic infection), also resulting in a lowered impact on prokaryotic communities, which shift towards (chemo)autotrophic assemblages, with lower organic matter consumption. Taken together, these results suggest that ocean acidification exerts a deep control on microbial benthic assemblages, with important feedbacks on ecosystem functioning.

Linking prokaryotic community composition to carbon biogeochemical cycling across a tropical peat dome in Sarawak, Malaysia

Tropical peat swamp forest is a global store of carbon in a water-saturated, anoxic and acidic environment. This ecosystem holds diverse prokaryotic communities that play a major role in nutrient cycling. A study was conducted in which a total of 24 peat soil samples were collected in three forest types in a tropical peat dome in Sarawak, Malaysia namely, Mixed Peat Swamp (MPS), Alan Batu (ABt), and Alan Bunga (ABg) forests to profile the soil prokaryotic communities through meta 16S amplicon analysis using Illumina Miseq. Results showed these ecosystems were dominated by anaerobes and fermenters such as Acidobacteria, Proteobacteria, Actinobacteria and Firmicutes that cover 80–90% of the total prokaryotic abundance. Overall, the microbial community composition was different amongst forest types and depths. Additionally, this study highlighted the prokaryotic communities’ composition in MPS was driven by higher humification level and lower pH whereas in ABt and ABg, the less acidic condition and higher organic matter content were the main factors. It was also observed that prokaryotic diversity and abundance were higher in the more oligotrophic ABt and ABg forest despite the constantly waterlogged condition. In MPS, the methanotroph Methylovirgula ligni was found to be the major species in this forest type that utilize methane (CH4), which could potentially be the contributing factor to the low CH4 gas emissions. Aquitalea magnusonii and Paraburkholderia oxyphila, which can degrade aromatic compounds, were the major species in ABt and ABg forests respectively. This information can be advantageous for future study in understanding the underlying mechanisms of environmental-driven alterations in soil microbial communities and its potential implications on biogeochemical processes in relation to peatland management.

Changes in Activity and Community Composition Shape Bacterial Responses to Size-Fractionated Marine DOM

To study the response of bacteria to different size-fractions of naturally occurring dissolved organic matter (DOM), a natural prokaryotic community from North Atlantic mesopelagic waters (1000 m depth) was isolated and grown in (i) 0.1-μm filtered seawater (CONTROL), (ii) the low-molecular-weight (<1 kDa) DOM fraction (L-DOM), and (iii) the recombination of high- (>1 kDa) and low-molecular-weight DOM fractions (H + L-DOM), to test the potential effect of ultrafiltration on breaking the DOM size continuum. Prokaryotic abundance and leucine incorporation were consistently higher in the H + L-DOM niche than in the L-DOM and CONTROL treatments, suggesting a different interaction with each DOM fraction and the disruption of the structural DOM continuum by ultrafiltration, respectively. Rhodobacterales (Alphaproteobacteria) and Flavobacteriales (Bacteroidetes) were particularly enriched in L-DOM and closely related to the colored DOM (CDOM) fraction, indicating the tight link between these groups and changes in DOM aromaticity. Conversely, some other taxa that were rare or undetectable in the original bacterial community were enriched in the H + L-DOM treatment (e.g., Alteromonadales belonging to Gammaproteobacteria), highlighting the role of the rare biosphere as a seed bank of diversity against ecosystem disturbance. The relationship between the fluorescence of protein-like CDOM and community composition of populations in the H + L-DOM treatment suggested their preference for labile DOM. Conversely, the communities growing on the L-DOM niche were coupled to humic-like CDOM, which may indicate their ability to degrade more reworked DOM and/or the generation of refractory substrates (as by-products of the respiration processes). Most importantly, L- and/or H + L-DOM treatments stimulated the growth of unique bacterial amplicon sequence variants (ASVs), suggesting the potential of environmental selection (i.e., changes in DOM composition and availability), particularly in the light of climate change scenarios. Taken together, our results suggest that different size-fractions of DOM induced niche-specialization and differentiation of mesopelagic bacterial communities.

Regulation of Microbial Activity Rates by Organic Matter in the Ross Sea during the Austral Summer 2017

The active prokaryotic communities proliferate in the ecosystems of the Antarctic Ocean, participating in biogeochemical cycles and supporting higher trophic levels. They are regulated by several environmental and ecological forcing, such as the characteristics of the water masses subjected to global warming and particulate organic matter (POM). During summer 2017, two polynyas in the Ross Sea were studied to evaluate key-microbiological parameters (the proteasic, glucosidasic, and phosphatasic activities, the microbial respiratory rates, the prokaryotic abundance and biomass) in relation to quantitative and qualitative characteristics of POM. Results showed significant differences in the epipelagic layer between two macro-areas (Terra Nova Bay and Ross Sea offshore area). Proteins and carbohydrates were metabolized rapidly in the offshore area (as shown by turnover times), due to high enzymatic activities in this zone, indicating fresh and labile organic compounds. The lower quality of POM in Terra Nova Bay, as shown by the higher refractory fraction, led to an increase in the turnover times of proteins and carbohydrates. Salinity was the physical constraint that played a major role in the distribution of POM and microbial activities in both areas.

Alternation of heterotrophic bacterial and archaeal production along nitrogen and salinity gradients in coastal wetlands

Coastal wetlands are valuable ecosystems with high biological productivity and diversity, which provide ecosystem services such as a reduction in the inputs of nitrogen into coastal waters, and storage of organic carbon, thus, acting as net carbon sinks. The rise of sea level as a consequence of climatic warming will salinize many coastal wetlands, but there is considerable uncertainty about how salinization will affect microbial communities and biogeochemical processes. We analyzed prokaryotic abundance and heterotrophic bacterial and archaeal production in 112 ponds within nine coastal wetlands from the western Mediterranean coast. We determined the main drivers of prokaryotic abundance and production in these wetlands using generalized linear models (GLMs). The best GLM, including all the coastal wetlands, indicated that the concentration of total dissolved nitrogen (TDN) positively affected the abundance of heterotrophic prokaryotes and heterotrophic archaeal production. In contrast, heterotrophic bacterial production was negatively related to TDN. This negative relationship appeared to be mediated by salinity and virus abundance. Heterotrophic bacterial production declined as salinity, and virus abundance, increased. We observed a switch from heterotrophic bacterial production towards heterotrophic archaeal production as salinity and virus abundance increased. Our results imply that microbial activity will change from bacterial-dominated processes to archaeal-dominated processes along with increases of nitrogen inputs and salinity. However, more studies are required to link the mineralization rates of dissolved nitrogen and organic carbon with specific archaeal taxa, to enable more accurate predictions on future scenarios of wetlands salinization and anthropogenic nitrogen inputs.

The Impact of a Fish Cannery Wastewater Discharge on the Bacterial Community Structure and Sanitary Conditions of Marine Coastal Sediments

The effects of fish cannery discharge (FCD) on bacteria in marine coastal sediments were investigated. Redox potentials were measured, and granulometry was determined by wet ASTM sieving, and with the Sedigraph method. Prokaryotic abundance (PA) was determined by epifluorescence microscopy (DAPI staining), and faecal indicator bacteria (FIB) enumerated with the multiple test tube and most probable number method. Total lipids were determined gravimetrically, and sterols analysed by GC/MSD. Bacterial community composition was determined after total DNA isolation, Illumina MiSeq amplification, and SILVAngs processing pipeline. The FCD was rich in lipids, heterotrophic prokaryotes and FIB. The bacterial community of the FCD was dominated by Firmicutes and Gammaproteobacteria and many potentially pathogenic bacteria. Highly porosusgravelly sands clogged with fish remains transitioned to less permeable sandy muds away from the FCD. All sediments were anoxic with extremely negative potentials around the outfall. High surface PA and FIB spread 300 m from the outfall. Gammaproteobacteria and Deltaproteobacteria appeared in all sediments. Sulfurovum and Anaerolineaceae characterized the most polluted locations where gammaproteobacterial Woeseiaceae/JTB255 marine benthic group declined. Gammaproteobacteria and Bacteroidetes characterized surface sediments, while Chloroflexi and Deltaproteobacteria prevailed in deeper layers. The FCD enriched sediments in lipids and allochthonous bacteria degrading sanitary quality, lowering the permeability, redox potential, and bacterial diversity.

Biological and environmental drivers of deep-sea benthic ecosystem functioning in Canada’s Laurentian Channel Area of Interest (AOI)

Ongoing environmental changes and accelerating biodiversity loss raise concern and interest about the role of environmental factors and biodiversity in determining marine ecosystem functioning. This study aims to identify the main drivers of benthic ecosystem functioning in deep-sea sedimentary habitats in the Laurentian Channel Area of Interest (AOI), and in particular the role of sea pens (Pennatulacea) as potential keystone species in the area. Using the ROV ROPOS we collected sediment cores and measured environmental variables from 6 stations inside the AOI (depths 348–445m) in September 2017. Through 48-hours incubations and flux measurements (oxygen, inorganic nutrients), we estimated organic matter remineralization, a key benthic function. Preliminary analyses show no significant variation in fluxes among stations, despite significant differences in environmental variables However, the presence/absence of Pennatulacea inside the cores indicated some capability to enhance remineralization and particularly nitrification. Ongoing analyses will address sediment properties, macrofaunal biodiversity, prokaryotic abundance, and biological traits as drivers of remineralization. Shedding new light on the primary drivers of ecosystem functioning in the area will inform the design or monitoring strategies proposed for this AOI and offer new perspectives and tools for MPA design.

Biological and environmental drivers of deep-sea benthic ecosystem functioning in Canada’s Laurentian Channel Area of Interest (AOI)

Ongoing environmental changes and accelerating biodiversity loss raise concern and interest about the role of environmental factors and biodiversity in determining marine ecosystem functioning. This study aims to identify the main drivers of benthic ecosystem functioning in deep-sea sedimentary habitats in the Laurentian Channel Area of Interest (AOI), and in particular the role of sea pens (Pennatulacea) as potential keystone species in the area. Using the ROV ROPOS we collected sediment cores and measured environmental variables from 6 stations inside the AOI (depths 348–445m) in September 2017. Through 48-hours incubations and flux measurements (oxygen, inorganic nutrients), we estimated organic matter remineralization, a key benthic function. Preliminary analyses show no significant variation in fluxes among stations, despite significant differences in environmental variables However, the presence/absence of Pennatulacea inside the cores indicated some capability to enhance remineralization and particularly nitrification. Ongoing analyses will address sediment properties, macrofaunal biodiversity, prokaryotic abundance, and biological traits as drivers of remineralization. Shedding new light on the primary drivers of ecosystem functioning in the area will inform the design or monitoring strategies proposed for this AOI and offer new perspectives and tools for MPA design.