Benthic Microbial Communities Research Articles

Per-, poly-fluoroalkyl substances (PFASs) pollution in benthic riverine ecosystem: Integrating microbial community coalescence and biogeochemistry with sediment distribution

Per-, Poly-fluoroalkyl substances (PFASs) accumulation in benthic environments is mainly determined by material mixing and represents a significant challenge to river remediation. However, less attention has been paid to the effects of sediment distribution on PFASs accumulation, and how PFASs influence microbial community coalescence and biogeochemical processes. In order to identify correlations between PFASs distribution and benthic microbial community functions, we conducted a field study and quantified the ecological constrains of material transportation on benthic microorganisms. Perfluorohexanoic acid (PFHxA) contributed most to the taxonomic heterogeneity of both archaeal (12.199%) and bacterial (13.675%) communities. Genera Methanoregula (R2 = 0.292) and Bacillus (R2 = 0.791) were identified as indicators that respond to PFASs. Phylogenetic null modeling indicated that deterministic processes (50.0–82.2%) dominated in spatial assembly of archaea, while stochasticity (94.4–97.8%) dominated in bacteria. Furthermore, spatial mixing of PFASs influenced broadly in nitrogen cycling of archaeal genomes, and phosphorus mineralization of bacterial genomes (p < 0.05). Overall, we quantified the effect of PFASs on community assembly and highlighted the constrains of PFASs influence on benthic geochemical potentials, which may provide new insights into riverine remediation.

Marine signature taxa and core microbial community stability along latitudinal and vertical gradients in sediments of the deepest freshwater lake.

Lake Baikal is the deepest (~1.6 km) and most voluminous freshwater reservoir on Earth. Compared to plankton, its benthos remains poorly explored. Here, we ask whether latitude and/or depth determine benthic microbial community structure and how Baikal communities compare to those of other freshwater, brackish and marine sediments. To answer, we collected sediment upper layers (0-1 cm) across a ~600 km North-South transect covering the three basins of the lake and from littoral to bathybenthic depths (0.5-1450 m). Analysis of 16S and 18S rRNA gene amplicon sequences revealed communities with high richness and evenness where rare operational taxonomic units (OTUs) collectively dominated. Archaea represented up to 25% or prokaryotic sequences. Baikal sediments harbored typically marine eukaryotic and prokaryotic OTUs recently identified in some lakes (diplonemids, Bolidophyceae, Mamiellales, SAR202, marine-like Synechococcus, Pelagibacterales) but also SAR324, Syndiniales and Radiolaria. We hypothesize that, beyond the salinity barrier, adaptation to oligotrophy explains the presence of these otherwise typically marine lineages. Baikal core benthic communities were relatively stable across sites and seemed not determined by depth or latitude. Comparative analyses with other freshwater, brackish and marine prokaryotic sediment communities confirmed the distinctness of Baikal benthos, which include elements of similarity to marine and hydrothermally influenced systems.

Benthic microbial diversity trends in response to heavy metals in an oxygen-deficient eutrophic bay of the Humboldt current system offshore the Atacama Desert

Mejillones Bay is a coastal ecosystem situated in an oxygen-deficient upwelling area impacted by mining activities in the coastal desert region of northern Chile, where conspicuous microbial life develops in the sediments. Herein, heavy metal (loid)s (HMs) such as Cu, Pb, As, Zn, Al, Fe, Cd, Mo, Ni and V as well as benthic microbial communities were studied using spectrometry and iTag-16 S rRNA sequencing. Samples were taken from two contrasting sedimentary localities in the Bay named Punta Rieles (PR) and Punta Chacaya (PC) within 10–50 m water-depth gradient. PR sediments were organic matter rich (21.1% of TOM at 50 m) and overlaid with low-oxygen waters (<0.06 ml O2/L bottom layer) compared with PC. In general, HMs like Al, Ni, Cd, As and Pb tended to increase in concentration with depth in PR, while the opposite pattern was observed in PC. In addition, PR presented a higher number of unique families (72) compared to PC (35). Among the top ten microbial families, Desulfobulbaceae (4.6% vs. 3.2%), Flavobacteriaceae (2.8% vs. 2.3%) and Anaerolineaceae (3.3% vs. 2.3%) dominated in PR, meanwhile Actinomarinales_Unclassified (8.1% vs. 4.2%) and Sandaracinaceae (4.4% vs. 2.0%) were more abundant in PC. Multivariate analyses confirmed that water depth-related variation was a good proxy for oxygen conditions and metal concentrations, explaining the structure of benthic microbial assemblages. Cd, Ni, As and Pb showed uniformly positive associations with communities that represented the keystone taxa in the co-occurrence network, including Anaerolineaceae, Thiotrichaceae, Desulfobulbaceae, Desulfarculaceae and Bacteroidales_unclassified communities. Collectively, these findings provide new insights for establishing the ecological interconnections of benthic microorganisms in response to metal contamination in a coastal upwelling environment.

Genomics Tools and Microbiota: Applications to Response in Coastal Ecosystems

Abstract Microorganisms are central and cross-cutting to oil spill response strategies. Biodegradation mediated by indigenous microbial communities is the ultimate fate of the majority of petroleum (oil and gas) that enters the marine environment. Key ecosystem services provided by microbes, such as organic matter and nutrient cycling, may be adversely affected by oil contamination. The Deepwater Horizon (DWH) oil spill was the first large scale environmental disaster to which the methods of genomics were applied to determine microbial response to a major perturbation. Here we present a case study on coastal ecosystems to highlight the knowledge gained by application of genomics tools to interrogate mechanisms of petroleum hydrocarbon degradation and to elucidate impacts of oil exposure on ecosystem health and functioning. At Pensacola Beach, results showed that oiling led to a large increase in the growth of indigenous microbes in the form of a series of bacterial blooms. Oil contamination strongly selected for microbial groups capable of hydrocarbon degradation. Oil was degraded and benthic microbial communities returned to near baseline levels approximately one year after oil came ashore. These results indicate that when small particles (&amp;lt; 1 cm) of weathered light oil are buried in the coastal zone, biodegradation by indigenous microbial communities is sufficient for the rapid mitigation of oil contamination after a major spill, whereas larger sand-oil-aggregates take longer to completely degrade because of their unfavorable surface to volume ratio. “Operation Deep Clean” removed these aggregates and enhanced biodegradation insofar as many larger oil aggregates were broken down into smaller ones thereby increasing the surface area available for microbial attack. For environmental managers, these results suggest that biodegradation in beach sands is relatively rapid because oxygen can easily penetrate to the buried oil, and resources may be better placed elsewhere in environments where degradation is limited by oxygen availability or microbial access to hydrocarbons. While specialist microbial groups such as nitrifiers show promise as bioindicators of oil contamination in coastal ecosystems, more work is needed to further validate these biomarkers. Despite substantial progress, a predictive understanding of the fate and impacts of oil spills remains hampered by challenges in interpreting the in situ activity and ecosystem response of benthic microbial populations. To advance this understanding, a dedicated funding mechanism is needed to support fundamental research. A polyphasic approach is encouraged that employs metagenomics in the field along with cultivation and microcosm or mesocosm experiments in the laboratory. Further, research during future disasters would be greatly facilitated by improved coordination between the emergency responders directing mitigation efforts and scientists investigating the success of those efforts.

Assembly processes and source tracking of planktonic and benthic bacterial communities in the Yellow River estuary.

Estuaries connect rivers with the ocean and are considered transition regions due to the continuous inputs from rivers. Microbiota from different sources converge and undergo succession in these transition regions, but their assembly mechanisms along environmental gradients remain unclear. Here, we found that salinity had a stronger effect on planktonic than on benthic microbial communities, and the dominant planktonic bacteria changed more distinctly than the dominant benthic bacteria with changes in salinity. The planktonic bacteria in the brackish water came mainly from seawater, which was confirmed in the laboratory, whereas the benthic bacteria were weakly affected by salinity, which appeared to be a mixture of the bacteria from riverine and oceanic sediments. Benthic bacterial community assembly in the sediments was mainly controlled by homogeneous selection and almost unaffected by changes in salinity, the dominant assemblage processes for planktonic bacteria changed dramatically along the salinity gradient, from homogeneous selection in freshwater to drift in seawater. Our results highlight that salinity is the key driver of estuarine microbial succession and that salinity is more important in shaping planktonic than benthic bacterial communities in the Yellow River estuary.

Silicified Polybessurus from the Ediacaran Doushantuo Formation records microbial activities within marine sediments

Polybessurus, as a common element of the late Mesoproterozoic to early Neoproterozoic microfossil assemblages, has yet no confirmed record from post-Cryogenian strata. In this study, we report Polybessurus sp. from the Ediacaran Doushantuo Formation chert nodules in western Hubei Province, South China. Polybessurus specimens from the Doushantuo Formation are identical to their pre-Cryogenian counterparts in morphology (stacked concave lamellae), composition (organic matter), and preservational mode (silicification). The Doushantuo specimens generally have large tubes (average diameter ~157 μm, maximum diameter ~450 μm), and are often preserved separately and parallel to the bedding plane, whereas the pre-Cryogenian specimens have relatively small tubes (mostly thinner than 100 μm in diameter), and are often preserved gregariously and perpendicular to the bedding plane. Polybessurus may be formed by a variety of benthic micro-organisms, mainly cyanobacteria, e.g., stalk forming taxa like Cyanostylon and endolithic taxa like Solentia, that are capable of secreting EPS (extracellular polymeric substance) unidirectionally to push itself forward in the sediment. The producers of Polybessurus may have played a role in the benthic microbial community by making microburrows, affecting textures and microenvironments of inshore sediments. As the first unambiguous record of Polybessurus from Ediacaran strata, our new findings extend its distribution from the late Mesoproterozoic–early Neoproterozoic to the late Neoproterozoic.

Columnar microbialites of the upper Miocene of Mallorca (Spain): A new morphogenetic model based on concurrent accretion and bioturbation – uncommon or overlooked?

AbstractBioturbation has long been considered an antagonist of microbialite development and preservation, because metazoan grazing and burrowing destroy benthic microbial communities. However, metazoan bioturbation, in conjunction with microbial accretion, may have had a significant role in the morphogenesis of some columnar microbialites, as suggested by the case study presented and by some Phanerozoic and Upper Proterozoic analogues discussed here. Late Miocene in age, the studied microbial biostrome developed in a western Mediterranean restricted shallow‐water platform dominated by grainy sediments and with a notable influence of bioturbation. This study is focused on the complex accretionary history of the columnar microbialite biostrome and on its striking dark grey colour, which is attributed to Mn‐oxyhydroxides precipitated during meteoric diagenesis linked to subaerial exposure. The characteristic columnar structure of the microbialite biostrome has features consistent with an accretionary origin of the columns, but also has features suggesting metazoan disruption. Therefore, a new morphogenetic model for columnar microbialites is presented, highlighting the concomitant roles of microbial accretion, bioturbation and grainy sediment infill of the intercolumn space. Whether this model is an exception or a rule, should be tested on other examples of Phanerozoic and Upper Proterozoic columnar microbialites. Nevertheless, this model is a step forward in understanding the complex microbe–metazoan interactions as constructive coexistence rather than just as destructive competition.

Biogeographic structuring of benthic microbial communities influence the establishment of global bioindicators for coastal aquaculture impact monitoring

With an increasing demand for finfish from aquaculture, the importance of monitoring the impact of aquaculture installations on coastal ecosystems becomes more and more important. The traditional approach employs macroinvertebrates as bioindicators to assess the ecological quality (EQ) of near-field benthic ecosystem, which is costly and time consuming. Modern approaches using environmental DNA metabarcodes of microbial organisms (eukaryotes and prokaryotes) have shown to be a powerful alternative. It is crucial that the ecological quality determined by molecular bioindicator signatures mirrors the results of standard macroinvertebrate inventories. Previous studies looking for bioindicators of organic enrichment have so far only analyzed samples within a specific geographic location (e.g. one farm, farms from one country). To answer the question if there are global bioindicators (or core communities) across different biogeographic regions, we analyzed 328 samples from three salmon producing countries (Norway, New Zealand, Scotland) to find commonalities in bacterial and ciliate DNA metabarcodes communities within the same ecological quality groups. We used supervised machine learning (SML) to predict both country origin and ecological status for both bacterial and ciliate eDNA markers. We then investigated if prediction accuracy for ecological quality increases if the dataset is reduced to single-country or two-country subsets to eliminate country/region specific effects. Further, core communities including only cosmopolitan ASVs were tested to detect possible global bioindicators for each individual EQ class. Based on the obtained results, we discuss the potential of a globally applicable database and a global training of an SML algorithm to predict ecological quality in aquafarm sediments using eDNA metabarcodes from benthic bacterial and ciliate communities.

Benthic prokaryotic microbial community assembly and biogeochemical potentials in E.coli - Stressed aquatic ecosystems during plant decomposition.

Benthic microbes play a crucial role in maintaining the biogeochemical balance of aquatic ecosystems especially the material cycling during plant decomposition. However, those systems in agricultural area are always threatened by agricultural run-off containing a mass of typical pathogenic invader- Escherichia coli. It is therefore vital to clarify the turnover, assembly, and geochemical functions of the E.coli invaded benthic prokaryotic microbial community during plant decomposition. During the decaying process, the key filtering factors of benthic community assembly were NH4+-N (P<0.001), NO2--N (P<0.01), and Organic-N (P<0.05). The E.coli colonized significantly in sediments (P<0.001) and drove the turnover of the bacterial community (P=0.001), which enhanced archaeal dominance in the benthic microbial network. E.coli also triggered niche structural variations. The biomass (%) of benthic nutrient cycling genera including Dechloromonas, Pseudomonas, Bacteroides, Candidatus_Methanofastidiosum, and Desulfomicrobium (P<0.05) was altered by E.coli stress. The structural equation model illustrated that E.coli critically affected the benthic microbial geochemical functions in multiple pathways (P<0.05). Our results provide new insights into benthic prokaryotic microbial community assembly and nutrient cycling and management under pollution stress.

Patterns in Benthic Microbial Community Structure Across Environmental Gradients in the Beaufort Sea Shelf and Slope.

The paradigm of tight pelagic-benthic coupling in the Arctic suggests that current and future fluctuations in sea ice, primary production, and riverine input resulting from global climate change will have major impacts on benthic ecosystems. To understand how these changes will affect benthic ecosystem function, we must characterize diversity, spatial distribution, and community composition for all faunal components. Bacteria and archaea link the biotic and abiotic realms, playing important roles in organic matter (OM) decomposition, biogeochemical cycling, and contaminant degradation, yet sediment microbial communities have rarely been examined in the North American Arctic. Shifts in microbial community structure and composition occur with shifts in OM inputs and contaminant exposure, with implications for shifts in ecological function. Furthermore, the characterization of benthic microbial communities provides a foundation from which to build focused experimental research. We assessed diversity and community structure of benthic prokaryotes in the upper 1 cm of sediments in the southern Beaufort Sea (United States and Canada), and investigated environmental correlates of prokaryotic community structure over a broad spatial scale (spanning 1,229 km) at depths ranging from 17 to 1,200 m. Based on hierarchical clustering, we identified four prokaryotic assemblages from the 85 samples analyzed. Two were largely delineated by the markedly different environmental conditions in shallow shelf vs. upper continental slope sediments. A third assemblage was mainly comprised of operational taxonomic units (OTUs) shared between the shallow shelf and upper slope assemblages. The fourth assemblage corresponded to sediments receiving heavier OM loading, likely resulting in a shallower anoxic layer. These sites may also harbor microbial mats and/or methane seeps. Substructure within these assemblages generally reflected turnover along a longitudinal gradient, which may be related to the quantity and composition of OM deposited to the seafloor; bathymetry and the Mackenzie River were the two major factors influencing prokaryote distribution on this scale. In a broader geographical context, differences in prokaryotic community structure between the Beaufort Sea and Norwegian Arctic suggest that benthic microbes may reflect regional differences in the hydrography, biogeochemistry, and bathymetry of Arctic shelf systems.

The degradation of di-(2-ethylhexyl) phthalate, DEHP, in sediments using percarbonate activated by seaweed biochars and its effects on the benthic microbial community

Di-(2-ethylhexyl) phthalate (DEHP) is a highly toxic and persistent contaminant. Elimination of DEHP from the environment is crucial to safe guard ecological and human health. Red seaweed-derived biochar (RSB), made from Agardhiella subulata residues, was used to activate sodium percarbonate (SPC) for the degradation of DEHP in contaminated estuarine surface sediments. The RSB was characterized by scanning transmission electron microscope-energy dispersive X-ray spectroscopy (STEM-EDS), micro-attenuated total reflectance-Fourier transform infrared spectroscopy (MATR-FTIR), elemental analysis (EA), thermogravimetric analysis (TGA), X-ray photoelectron spectrometry (XPS), linear sweep voltammetry (LSV), and Tafel measurements. Results revealed that the increase in SPC dosage, specifically, [DEHP] to [SPC] molar ratio of 1:1000, increased DEHP removal in the sediment. The pyrolysis temperature (300–900 °C) for biochar preparation significantly controlled the particle size and catalytic capacity of RSB. Pristine RSB contributed catalytic sites, which effectively activated SPC via electron transfer through the RSB matrix, that generated HO• and facilitated the carbocatalysis degradation of DEHP. RSB900 was the best-performing SPC activator. Under the optimal initial pH of 9, total DEHP degradation was 63% in 12 h. Treatment with RSB and SPC, significantly increased the bacterial abundance in the sediment. Results of next-generation sequencing analyses showed that Proteobacteria and Bacterioidetes were the dominant bacterial phyla. The microbial abundance and diversity of the sediment ecosystems were improved significantly upon treatment by the RSB–SPC process, indicating the efficacy of the remediation technology. Results provide valuable insights into the role of microbial communities as indicators of sediment quality.

Insights into the microbial autotrophic potential of a shallow oligotrophic alpine pond

Carbon dioxide fixation is one of the most important biogeochemical processes worldwide, but our current understanding of the distribution of microbial autotrophy and its ecological significance in oligotrophic freshwater systems, and particularly in benthic habitats, is poor and limited primarily to photoautotrophic organisms. In this study we investigated the autotrophic microbial communities inhabiting the sediments of a high-elevation, oligotrophic freshwater pond in the north-western Italian Alps. The abundance and distribution of three different forms of the ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) large-subunit gene (cbbLG, Form I green-like; cbbLR, Form I red-like; cbbM, Form II) were assessed in samples collected at different depths by quantitative polymerase chain reaction (qPCR); correlations with sediment geochemical properties and total bacterial abundance were also examined. RuBisCO forms cbbLG, cbbLR and cbbM were all detected, with abundances of 9.13–10.90, 6.93–8.77 and 6.75–7.93 log(copies) g–1 dry weight respectively. For all the RuBisCO genes, interannual variability overcame depth-related variability. The abundance of RuBisCO genes was strongly correlated with total bacterial abundance, and both were positively correlated with Ca2+ and Mg2+ concentrations. These observations provide some first indications of the distribution of photo- and chemolithoautotrophic bacteria relying on the Calvin–Benson–Bassham cycle for C fixation in alpine pond sediments, and suggest that they may represent an important component of the total benthic microbial community.

Microbial Diversity of Pinnacle and Conical Microbial Mats in the Perennially Ice-Covered Lake Untersee, East Antarctica.

Antarctic perennially ice-covered lakes provide a stable low-disturbance environment where complex microbially mediated structures can grow. Lake Untersee, an ultra-oligotrophic lake in East Antarctica, has the lake floor covered in benthic microbial mat communities, where laminated organo-sedimentary structures form with three distinct, sympatric morphologies: small, elongated cuspate pinnacles, large complex cones and flat mats. We examined the diversity of prokaryotes and eukaryotes in pinnacles, cones and flat microbial mats using high-throughput sequencing of 16S and 18S rRNA genes and assessed how microbial composition may underpin the formation of these distinct macroscopic mat morphologies under the same environmental conditions. Our analysis identified distinct clustering of microbial communities according to mat morphology. The prokaryotic communities were dominated by Cyanobacteria, Proteobacteria, Verrucomicrobia, Planctomycetes, and Actinobacteria. While filamentous Tychonema cyanobacteria were common in all mat types, Leptolyngbya showed an increased relative abundance in the pinnacle structures only. Our study provides the first report of the eukaryotic community structure of Lake Untersee benthic mats, which was dominated by Ciliophora, Chlorophyta, Fungi, Cercozoa, and Discicristata. The eukaryote richness was lower than for prokaryote assemblages and no distinct clustering was observed between mat morphologies. These findings suggest that cyanobacterial assemblages and potentially other bacteria and eukaryotes may influence structure morphogenesis, allowing distinct structures to form across a small spatial scale.

Nitrogen cycling in coastal sediment microbial communities with seasonally variable benthic nutrient fluxes

Benthic microbial communities contribute to nitrogen (N) cycling in coastal ecosystems through taxon-specific processes such as anammox, nitrification and N-fixation and community attributed pathways such as denitrification. By measuring the total (DNA-based) and active (RNA-based) surface sediment microbial community composition and the abundance and activity profiles of key N-cycling genes in a semi-enclosed embayment—Port Phillip Bay (PPB), Australia—we show that although the total relative abundance of N-cycling taxa is comparatively lower close to estuary inputs (Hobsons Bay [HB]), the capacity for this community to perform diverse Ncycling processes is comparatively higher than in sediments isolated from inputs (Central PPB [CPPB]). In HB, seasonal structuring of the sediment microbial community occurred between spring and summer, co-occurring with decreases in the activity profiles of anammox bacteria and organic carbon content. No changes were detected in the activity profiles of nitrifiers or the community-based pathway denitrification. Although no seasonal structuring of the sediment microbial community occurred in CPPB, the activity profiles of key N-cycling genes displayed comparatively higher within-site variability. These results show that despite N-cycling taxa representing a smaller fraction of the total community composition in estuary impacted sediments (HB) these microbial communities consistently engage in N-cycling processes and that seasonal instability in the composition of this community is not reflective of changes in its capacity to cycle N through coupled nitrification-denitrification but potentially via changes within the anammox community.

Assessing the Diversity of Benthic Sulfate-Reducing Microorganisms in Northwestern Gulf of Mexico by Illumina Sequencing of dsrB Gene.

This study investigates the community composition, structure, and abundance of sulfate-reducing microorganisms (SRM) in surficial sediments of the Northwestern Gulf of Mexico (NWGoM) along a bathymetric gradient. For these purposes, Illumina sequencing and quantitative PCR (qPCR) of the dissimilatory sulfite reductase gene beta subunit (dsrB gene) were performed. Bioinformatic analyses indicated that SRM community was predominantly composed by members of Proteobacteria and Firmicutes across all the samples. However, Actinobacteria, Thermodesulfobacteria, and Chlorobi were also detected. Phylogenetic analysis indicated that unassigned dsrB sequences were related to Deltaproteobacteria and Nitrospirota superclusters, Euryarchaeota, and to environmental clusters. PCoA ordination revealed that samples clustered in three different groups. PERMANOVA indicated that water depth, temperature, redox, and nickel and cadmium content were the main environmental drivers for the SRM communities in the studied sites. Alpha diversity and abundance of SRM were lower for deeper sites, suggesting decreasing sulfate reduction activity with respect to water depth. This study contributes with the understanding of distribution and composition of dsrAB-containing microorganisms involved in sulfur transformations that may contribute to the resilience and stability of the benthic microbial communities facing metal and hydrocarbon pollution in the NWGoM, a region of recent development for oil and gas drilling.

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).

PALAEOENVIRONMENTAL CONTEXTS FOR MICROBIAL COMMUNITIES FROM Fe-Mn CRUSTS OF MIDDLE-UPPER JURASSIC HARDGROUNDS (BETIC-RIFIAN CORDILLERA)

The Middle-Upper Jurassic transition within the External Subbetic (Betic Cordillera) and the Jbel Moussa Group (Rifian Calcareous Chain) is characterised by numerous stratigraphic breaks recorded as palaeoreliefs, omission surfaces and hardgrounds. One common characteristic is the presence of microbial Fe-Mn crusts and Mn crusts. Three different contexts of microbially mediated Fe-Mn crusts can be distinguished: a) hydrogenetic surficial Fe-Mn crusts and macro-oncoids, b) hydrogenetic cryptic Fe-Mn crusts, and c) hydrothermal surficial Mn crusts. Encrusting foraminifera (Thurammina, Placopsilina, Tolypammina and nubeculariids) and fungi fed on bacteria, while the bacteria and fungi took advantage of the nutrient-rich foraminiferal excretions. The cryptic Fe-Mn crusts are also hydrogenetic crusts developed in the walls of submarine cavities and fractures in the External Subbetic at the time of the hardground development. They are endostromatolites consisting almost exclusively of Frutexites in the case of thin neptunian dykes, or serpulid-Frutexites assemblages in a large neptunian sill. This assemblage reflects the colonization of unfavourable environment (aphotic with low oxygenation) as a response to the photophobic behaviour of chemosynthetic and cryptobiontic microorganisms. Finally, the hydrothermal Mn crusts registered in the Rif are characterised by the record of bacillus-shaped bacteria and different type of filaments. The precipitation of manganese minerals is interpreted as induced by the chemo-organotrophic behaviour of benthic microbial communities, since manganese oxides may form as a result of the direct metabolic activity of bacteria in hydrothermal environments. Very well-preserved fungal hyphae evidence the presence of fungi that probably fed on bacterial communities and their by-products

'Candidatus Oscillochloris kuznetsovii' a novel mesophilic filamentous anoxygenic phototrophic Chloroflexales bacterium from Arctic coastal environments.

Chloroflexales bacteria are mostly known as filamentous anoxygenic phototrophs that thrive as members of the microbial communities of hot spring cyanobacterial mats. Recently, we described many new Chloroflexales species from non-thermal environments and showed that mesophilic Chloroflexales are more diverse than previously expected. Most of these species were isolated from aquatic environments of mid-latitudes. Here, we present the comprehensive characterization of a new filamentous multicellular anoxygenic phototrophic Chloroflexales bacterium from an Arctic coastal environment (Kandalaksha Gulf, the White Sea). Phylogenomic analysis and 16S rRNA phylogeny indicated that this bacterium belongs to the Oscillochloridaceae family as a new species. We propose that this species be named 'Candidatus Oscillochloris kuznetsovii'. The genomes of this species possessed genes encoding sulfide:quinone reductase, the nitrogenase complex and the Calvin cycle, which indicate potential for photoautotrophic metabolism. We observed only mesophilic anaerobic anoxygenic phototrophic growth of this novel bacterium. Electron microphotography showed the presence of chlorosomes, polyhydroxyalkanoate-like granules and polyphosphate-like granules in the cells. High-performance liquid chromatography also revealed the presence of bacteriochlorophylls a, c and d as well as carotenoids. In addition, we found that this bacterium is present in benthic microbial communities of various coastal environments of the Kandalaksha Gulf.

Temporal Changes in Microbial Communities Beneath Fish Farm Sediments Are Related to Organic Enrichment and Fish Biomass Over a Production Cycle

The marine fish farming industry is growing at a significant rate, yet a number of concerns still remain with regards to environmental impacts on the surrounding coastal sea and its biota. Here, we assessed the impact of intensive farming on benthic prokaryotic communities at a Mediterranean sea bass and sea bream intensive aquaculture site over a period of 10 months, in relation to the increase in fish biomass within the cage together with the organic matter enrichment in the sediments. We report positive relationships between prokaryotic abundance and both organic matter and fish biomass, and a contextual decrease in prokaryotic diversity below the cages. A significant shift in microbial community composition occurred in fish farm sediments (FF) over time, indicating a likely impact of ongoing aquaculture activity on prokaryotic communities. Among the dominant taxa at the impacted site, we found Epsilonproteobacteria and Bacteroidetes, which showed a general increase with fish biomass. Analyses on specialist taxa underlined significant contributions of Clostridiales and Bacteroidales in the farmed sediments. Finally, sea bream and sea bass gut microbiome-related taxa were detected during the sampling period. Our results indicate that prokaryotic community composition underneath the cages is related to fish biomass and organic enrichment over the course of production, and confirms that the study of benthic microbial communities at aquaculture sites represents a useful tool to assess the impact of intensive mariculture on the surrounding environment.

Biological Natural Attenuation and Contaminant Oxidation in Sediment Caps: Recent Advances and Future Opportunities

Capping represents an efficient and well-established remediation practice to contain pollutants in sediments. Coupling capping amendments with biodegradation is an emerging technology with great potential to promote simultaneous sequestration and oxidation of contaminants in situ. Capping materials alter the native sediment environment and affect the biodegradation potential of benthic microbial communities. The placement of materials specifically influences (i) porewater pH and composition, (ii) nutrient fluxes, (iii) electron accepting processes, (iv) bioavailability of contaminants, and (v) biofilm formation. This review summarizes current literature documenting the impact of these alterations on microbial ecology and biodegradation activity, describes recent advances in bioactive sediment caps, and identifies areas where additional research is warranted.