Characterization of the anaerobic microbial community in oil-polluted subtidal sediments: aromatic biodegradation potential after thePrestigeoil spill

Anaerobaca lacustris gen. nov., sp. nov., an obligately anaerobic planctomycete of the widespread SG8-4 group, isolated from a coastal lake, and proposal of Anaerobacaceae fam. nov

One of the numerous and widespread lineages of planctomycetes is the hitherto uncultured SG8-4 group inhabiting anoxic environments. A novel anaerobic, mesophilic, alkalitolerant, chemoorganotrophic bacterium (strain M17dextrT) was isolated from anaerobic sediment of a coastal lake (Taman Peninsula, Russia). The cell were mainly non-motile cocci, 0.3 to 1.0 µm in diameter forming chains or aggregates. The cells had a Gram-negative cell wall and divided by binary fission. The temperature range for growth was 20-37 0C (optimum at 30 0C). The pH range for growth was 6.5-10.0, with an optimum at pH 8.0-8.5. Strain M17dextrT fermented mono-, di- and polysaccharides (starch, xanthan gum, dextran, N-acetylglucosamine), but did not utilized proteinaceous compounds. Major cellular fatty acids were C16:0 and C18:0. The genome of strain M17dextrT had a size of 5.7 Mb with a G + C content of 62.49 %. The genome contained 345 CAZyme genes. The closest cultured phylogenetic relatives of strain M17dextrT were members of the order Sedimentisphaerales, class Phycisphaerae. Among characterized planctomycetes, the highest 16S rRNA gene sequence similarity (88.3 %) was observed with Anaerohalosphaera lusitana. According to phylogenomic analysis strain M17dextrT together with many uncultured representatives of Sedimentisphaerales forms a separate family-level lineage. We propose to assign strain M17dextrT to a novel genus and species, Anaerobaca lacustris gen. nov., sp. nov.; the type strain is M17dextrT (=VKM B-3571 T = DSM 113417 T = JCM 39238 T = KCTC 25381 T = UQM 41474 T). This genus is placed in a novel family, Anaerobacaceae fam. nov. within the order Sedimentisphaerales.

Analysis of the metals and metalloids concentrations and of the bacterial population in sediments of the Red River Delta, Vietnam

In this study, we discuss for the first time the relationships between the diversity of the bacterial population and of the metals and metalloids concentrations in the sediments of the Red River Delta, Vietnam. The analysis of the 16S rRNA by the Illumina technology revealed a diversified population and a potential of bioremediation by the microorganisms, notably by the Bacilli relatively abundant in the Bach Dang estuary, where high metals and metalloids concentrations were highlighted. This work offers new information on the environmental context of the delta and highlights the potential impact that metals and metalloids may have on the bacterial population. Further investigations on the role of the bacteria in the biogeochemistry of this ecosystem will be of interest for the development of bioremediation processes.

Heavy metal induced shifts in microbial community composition and interactions with dissolved organic matter in coastal sediments

Heavy metals can impact the structure and function of coastal sediment. The dissolved organic matter (DOM) pool plays an important role in determining both the heavy metal toxicity and microbial community composition in coastal sediments. However, how heavy metals affect the interactions between microbial communities and DOM remains unclear. Here, we investigated the influence of heavy metals on the microbial community structure (including bacteria and archaea) and DOM composition in surface sediments of Beibu Gulf, China. Our results revealed firstly that chromium, zinc, cadmium, and lead were the heavy metals contributing to pollution in our studied area. Furthermore, the DOM chemical composition was distinctly different in the contaminated area from the uncontaminated area, characterized by a higher average O/C ratio and increased prevalence of carboxyl-rich alicyclic molecules (CRAM) and highly unsaturated compounds (HUC). This indicates that DOM in the contaminated area was more recalcitrant compared to the uncontaminated area. Except for differences in archaeal diversity between the two areas, there were no significant variations observed in the structure of archaea and bacteria, as well as the diversity of bacteria, across the two areas. Nevertheless, our co-occurrence network analysis revealed that the B2M28 and Euryarchaeota, dominating bacterial and archaeal groups in the contaminated area were strongly related to CRAM. The network analysis also unveiled correlations between active bacteria and elevated proportions of nitrogen-containing DOM molecules. In contrast, the archaea-DOM network exhibited strong associations with nitrogen- and sulfur-containing molecules. Collectively, these findings suggest that heavy metals indeed influence the interaction between microbial communities and DOM, potentially affecting the accumulation of recalcitrant compounds in coastal sediments.

Accelerated deterioration corrosion of X70 steel by oxidation acid-producing process catalyzed by Acinetobacter soli in oil-water environment

Deterioration corrosion occurs between the external surface of oil pipelines and aerobic oil-degrading microorganisms in oil fields. Microorganisms with aerobic oil pollution remediation capabilities may catalyze more serious anaerobic microbial corrosion due to the carbon source supply. In this study, Acinetobacter soli strains were isolated from oil-contaminated environments, and their role in the deterioration corrosion behavior of X70 steel in an oil-water environment was investigated using the EDS multipoint scanning method. The presence of oil controls the deposition of carbon and phosphorus and diffusion of oxygen, leading to significant adhesion attraction and initial growth inhibition of biofilm on the metal surface. A. soli facilitates oxygen transfer and iron ion dissolution, thereby accelerating the pitting corrosion of X70 steel. This corrosion of the X70 steel, in turn, further accelerates the microbial degradation of oil, inhibiting the appearance of calcareous scale in the later stage of corrosion. The corrosion of X70 steel is influenced by microbial degradation, and the specific corrosion behaviors are related to the activity of A. soli in the petroleum environment. This study sheds light on the corrosion mechanisms of X70 steel by A. soli at different stages, providing insights into the interactions between microorganisms, oil pollution, and metal corrosion in oil fields.

Comparative evaluation and prioritization of key influences on biodegradation of 2,2',4,4'-tetrabrominated diphenyl ether by bacterial isolate B. xenovorans LB400

Polybrominated diphenyl ethers (PBDEs) are a class of persistent organic pollutants being widely distributed and harmful to human health and wildlife, and the development of sustainable rehabilitation strategies including microbial degradation is of great concern. Although the increasing number of bacteria, especially the broad-spectrum and potent aerobes have been isolated for the efficient removal of PBDEs, the external influences and the corresponding influential mechanism on biodegradation are not fully understood yet. Given the wide-spectrum biodegradability of aerobic bacterial isolate, B. xenovorans LB400 for PBDEs, the dual impacts of many pivotal factors including pH, temperature, presence of dissolved organic matter (DOM) and cadmium ion etc. were comprehensively revealed on biodegradation of 2,2',4,4'-tetrabromodiphenyl ether (BDE-47). Due to the structural resemblance and stimulation of specific enzyme activity in bacteria, the biphenyl as substrates showed the greater capacity than non-aromatic compounds in improving biodegradation. The individual adaptation to neutrality and cultivation at about 30 °C was beneficial for biodegradation since the bacterial cellular viability and enzyme activity was mostly preserved. Although it was possibly good for the induction of hormesis and favorable to enhance the permeability or bioavailability of pollutant, the exceeding increase of Cd²⁺ or DOM may not give the profitable increase of biodegradation yet for the detrimental effect. For biodegradation, the mechanistic relationship that took account of the integrative correlation with the influential factors was artfully developed using partial least square (PLS) regression technique. Relative to the most significant influence of culture time and initial concentration of BDE-47, the larger relevance of other factors primarily marked as pH and DOM was consecutively shown after the quantitative prioritization. This may not only help understand the influential mechanism but provide a prioritizing regulation strategy for biodegradation of BDE-47. The PLS-derived relationship was validated with the certain predictability in biodegradation, and could be used as an alternative to accelerate a priori evaluation of suitability or improve the feasibility of such bacteria in remediation of PBDEs in the environment.

Influence of Extremely High Pressure and Oxygen on Hydrocarbon-Enriched Microbial Communities in Sediments from the Challenger Deep, Mariana Trench

Recent studies reported that highly abundant alkane content exists in the ~11,000 m sediment of the Mariana Trench, and a few key alkane-degrading bacteria were identified in the Mariana Trench. At present, most of the studies on microbes for degrading hydrocarbons were performed mainly at atmospheric pressure (0.1 MPa) and room temperature; little is known about which microbes could be enriched with the addition of n-alkanes under in-situ environmental pressure and temperature conditions in the hadal zone. In this study, we conducted microbial enrichments of sediment from the Mariana Trench with short-chain (SCAs, C7–C17) or long-chain (LCAs, C18–C36) n-alkanes and incubated them at 0.1 MPa/100 MPa and 4 °C under aerobic or anaerobic conditions for 150 days. Microbial diversity analysis showed that a higher microbial diversity was observed at 100 MPa than at 0.1 MPa, irrespective of whether SCAs or LCAs were added. Non-metric multidimensional scaling (nMDS) and hierarchical cluster analysis revealed that different microbial clusters were formed according to hydrostatic pressure and oxygen. Significantly different microbial communities were formed according to pressure or oxygen (p < 0.05). For example, Gammaproteobacteria (Thalassolituus) were the most abundant anaerobic n-alkanes-enriched microbes at 0.1 MPa, whereas the microbial communities shifted to dominance by Gammaproteobacteria (Idiomarina, Halomonas, and Methylophaga) and Bacteroidetes (Arenibacter) at 100 MPa. Compared to the anaerobic treatments, Actinobacteria (Microbacterium) and Alphaproteobacteria (Sulfitobacter and Phenylobacterium) were the most abundant groups with the addition of hydrocarbon under aerobic conditions at 100 MPa. Our results revealed that unique n-alkane-enriched microorganisms were present in the deepest sediment of the Mariana Trench, which may imply that extremely high hydrostatic pressure (100 MPa) and oxygen dramatically affected the processes of microbial-mediated alkane utilization.

Microbial community niches on microplastics and prioritized environmental factors under various urban riverine conditions

Microplastics (MPs) provide habitats to microorganisms in aquatic environments; distinct microbial niches have recently been elucidated. However, there is little known about the microbial communities on MPs under urban riverine conditions, in which environmental factors fluctuate. Therefore, this study investigated MP biofilm communities under various urban riverine conditions (i.e., organic content, salinity, and dissolved oxygen (DO) concentration) and evaluated the prioritized factors affecting plastisphere communities. Nine biofilm-forming reactors were operated under various environmental conditions. Under all testing conditions, biofilms grew on MPs with decreasing bacterial diversity. Interestingly, biofilm morphology and bacterial populations were driven by the environmental parameters. We found that plastisphere community structures were grouped according to the environmental conditions; organic content in the water was the most significant factor determining MP biofilm communities, followed by salinity and DO concentration. The principal plastisphere communities were Proteobacteria, Bacteroidetes, Cyanobacteria, and Firmicutes phyla. In-depth analyses of plastisphere communities revealed that biofilm-forming and plastic-degrading bacteria were the predominant microbes. In addition, potential pathogens were majorly discovered in the riverine waters with high organic content. Our results suggest that distinct plastisphere communities coexist with MP particles under certain riverine water conditions, implying that the varied MP biofilm communities may affect urban riverine ecology in a variety of ways.

Bacterial community response to chronic heavy metal contamination in marine sediments of the East China Sea

Marine sediments act as a sink for various heavy metals, which may have profound impact on sedimentary microbiota. However, our knowledge about the collaborative response of bacterial community to chronic heavy metal contamination remains little. In this study, concentrations of seven heavy metals (As, Cd, Cr, Cu, Hg, Pb, and Zn) in sediments collected from the East China Sea were analyzed and Illumina Miseq 16 S rRNA sequencing was applied to characterize the structure of bacterial community. Microbiota inhabiting sediments in the East China Sea polluted with heavy metals showed different community composition from relatively pristine sites. The response of bacterial community to heavy metal stress was further interrogated with weighted correlation network analysis (WGCNA). WGCNA revealed ten bacterial modules exhibiting distinct co-occurrence patterns and among them, five modules were related to heavy metal pollution. Three of them were positively correlated with an increase in at least one heavy metal concentration, hubs (more influential bacterial taxa) of which were previously reported to be involved in the geochemical cycling of heavy metals or possess tolerance to heavy metals, while another two modules showed opposite patterns. Our research suggested that ecological functional transition might have occurred in East China Sea sediments by shifts of community composition with sensitive modules majorly involved in the meaningful global biogeochemical cycling of carbon, sulfur, and nitrogen replaced by more tolerant groups of bacteria due to long-term exposure to low-concentration heavy metals. Hubs may serve as indicators of perturbations of benthic bacterial community caused by heavy metal pollution and support monitoring remediation of polluted sites in marine environments.

Biodegradation potential of polycyclic aromatic hydrocarbons in Taihu Lake sediments

ABSTRACTTo assess the biodegradation potential of polycyclic aromatic hydrocarbons (PAHs) in sediments, sediment microcosms were constructed with sediments collected from six lake zones with different trophic statuses in Taihu Lake. The presence and concentration of PAH-degrading bacteria (PDB) were estimated by the most probable number (MPN) method. After 85 d of aerobic and anaerobic incubation, spiked PAHs (phenanthrene, pyrene, and benzo[a]pyrene) were partially degraded by indigenous sediment microorganisms. Large differences in PAH degradation were observed depending on the molecular size of the PAHs. The PAH removal efficiency in sediments under aerobic conditions was higher than that under anaerobic conditions. MPN analyses showed a higher abundance of degrading microflora in the high PAH-contaminated sites than in the low PAH-contaminated sites. Moreover, the anaerobic PDB populations in the sediments from the six different sites were much higher than those of aerobic PDB. The PAH biodegradation capability in sediments was associated with the geochemical conditions and bacterial populations. PDB showed a broad spatial distribution, thereby implying that they played an important role in the natural attenuation and cycling of PAHs in Taihu Lake. This work indicates that PAHs remain a concern in Taihu Lake sediments and can provide useful information for further bioremediation of PAH-contaminated sediments.

Ecological risk potentials of petroleum hydrocarbons and heavy metals shape the bacterial communities of marine hydrosphere at Atlantic Ocean, Atlas Cove, Nigeria

Trans-Atlantic voyage of petroleum often leads to marine pollution with petroleum hydrocarbons (PHs) and heavy metals (HMs) that defines structures of autochthonous bacteria in the hydrosphere. Bacterial taxa of marine sediments exposed to petroleum transport activities were profiled using 16S rDNA metagenomics and correlated with the geochemistry to establish their impact on the microbiome. The physico-chemistry of the marine systems revealed varied degrees of contamination with PHs and HMs exceeding recommended threshold for aquatic life. Ecological risk assessment based on organic carbon of the sediment established phenanthrene, anthracene, and pyrene posed high risks (index risk quotient >32) to marine life. The most dominant phylum of the 44 bacterial phyla in the marine-sphere was Proteobacteria with relative abundance of 45-77% in the sampling locations. Relative dominance of Proteobacteria in the sediments spanned Gammaproteobacteria (17-25%), Deltaproteobacteria (12-20%), and Alphaproteobacteria (7-14%). Whereas, more operational taxonomic units (OTUs) belonging to Epsilonproteobacteria (19 ± 2.4%) were found in estuarine sediment unlike < 0.5% relative abundances obtained from oceanic sediments. Sulfurimonas apparently dominated the bacterial genera with up to 2.16 ± 0.19% abundance in oceanic sediments. Canonical correspondence analysis revealed that PHs shaped the structure of bacterial OTUs in oceanic sediments where petroleum loading/offloading occurs unlike in some kilometres a yonder where HMs correlated with the bacteria structure. The dominant bacteria might possibly pivotal to ecophysiologies of hydrocarbon contaminated marine environment, and would be pertinent to biotechnological applications for possible bioremediation campaign.

Bacterial communities in temperate and polar coastal sands are seasonally stable

Coastal sands are biocatalytic filters for dissolved and particulate organic matter of marine and terrestrial origin, thus, acting as centers of organic matter transformation. At high temporal resolution, we accessed the variability of benthic bacterial communities over two annual cycles at Helgoland (North Sea), and compared it with seasonality of communities in Isfjorden (Svalbard, 78°N) sediments, where primary production does not occur during winter. Benthic community structure remained stable in both, temperate and polar sediments on the level of cell counts and 16S rRNA-based taxonomy. Actinobacteriota of uncultured Actinomarinales and Microtrichales were a major group, with 8 ± 1% of total reads (Helgoland) and 31 ± 6% (Svalbard). Their high activity (frequency of dividing cells 28%) and in situ cell numbers of >10% of total microbes in Svalbard sediments, suggest Actinomarinales and Microtrichales as key heterotrophs for carbon mineralization. Even though Helgoland and Svalbard sampling sites showed no phytodetritus-driven changes of the benthic bacterial community structure, they harbored significantly different communities (p < 0.0001, r = 0.963). The temporal stability of benthic bacterial communities is in stark contrast to the dynamic succession typical of coastal waters, suggesting that pelagic and benthic bacterial communities respond to phytoplankton productivity very differently.

Distinct microbial community along the chronic oil pollution continuum of the Persian Gulf converge with oil spill accidents

The Persian Gulf, hosting ca. 48% of the world's oil reserves, has been chronically exposed to natural oil seepage. Oil spill studies show a shift in microbial community composition in response to oil pollution; however, the influence of chronic oil exposure on the microbial community remains unknown. We performed genome-resolved comparative analyses of the water and sediment samples along Persian Gulf's pollution continuum (Strait of Hormuz, Asalouyeh, and Khark Island). Continuous exposure to trace amounts of pollution primed the intrinsic and rare marine oil-degrading microbes such as Oceanospirillales, Flavobacteriales, Alteromonadales, and Rhodobacterales to bloom in response to oil pollution in Asalouyeh and Khark samples. Comparative analysis of the Persian Gulf samples with 106 oil-polluted marine samples reveals that the hydrocarbon type, exposure time, and sediment depth are the main determinants of microbial response to pollution. High aliphatic content of the pollution enriched for Oceanospirillales, Alteromonadales, and Pseudomonadales whereas, Alteromonadales, Cellvibrionales, Flavobacteriales, and Rhodobacterales dominate polyaromatic polluted samples. In chronic exposure and oil spill events, the community composition converges towards higher dominance of oil-degrading constituents while promoting the division of labor for successful bioremediation.

Molecular characterization of bacteria and archaea in a bioaugmented zero-water exchange shrimp pond

In the zero-water exchange shrimp culture pond maintained with the application of indigenous bioaugmentor, low levels of total ammonia–nitrogen were reported, indicating the relevance of indigenous microbial communities. Sediments (0–5 cm layer) were sampled from the pond (85th day) and the bacterial and archaeal communities; specifically, the ammonia oxidizers (ammonia-oxidizing bacteria, ammonia-oxidizing archaea, and anaerobic ammonia-oxidizing bacteria) in the sediment metagenome of the pond were analysed using the 16S rRNA and functional genes. Bacterial and archaeal 16S rRNA genes showed the relative abundance of Delta-Proteobacteria and Bacteroidetes groups performing sulphur respiration and organic matter degradation, archaeal groups of anaerobic sulphur respiring Crenarchaeotae, and chemolithoautotrophic ammonia oxidizers belonging to Thaumarchaeota. The presence of these diverse bacterial and archaeal communities denotes their significant roles in the cycling the carbon, nitrogen, and sulphur thereby bringing out efficient bioremediation in the bioaugmented zero-water exchange shrimp culture pond. Similarly, the functional gene-specific study showed the predominance of Nitrosomonas sp. (ammonia-oxidizing bacteria), Nitrosopumilus maritimus (ammonia-oxidizing archaea), and Candidatus Kuenenia (anaerobic ammonia-oxidizing bacteria) in the system, which points to their importance in the removal of accumulated ammonia. Thus, this study paves the way for understanding the microbial communities, specifically the ammonia oxidizers responsible for maintaining healthy and optimal environmental conditions in the bioaugmented zero-water exchange shrimp culture pond.

Trace Metal Contamination Impacts Predicted Functions More Than Structure of Marine Prokaryotic Biofilm Communities in an Anthropized Coastal Area

Trace metal (TM) contamination in marine coastal areas is a worldwide threat for aquatic communities. However, little is known about the influence of a multi-chemical contamination on both marine biofilm communities' structure and functioning. To determine how TM contamination potentially impacted microbial biofilms' structure and their functions, polycarbonate (PC) plates were immerged in both surface and bottom of the seawater column, at five sites, along strong TM contamination gradients, in Toulon Bay. The PC plates were incubated during 4 weeks to enable colonization by biofilm-forming microorganisms on artificial surfaces. Biofilms from the PC plates, as well as surrounding seawaters, were collected and analyzed by 16S rRNA amplicon gene sequencing to describe prokaryotic community diversity, structure and functions, and to determine the relationships between bacterioplankton and biofilm communities. Our results showed that prokaryotic biofilm structure was not significantly affected by the measured environmental variables, while the functional profiles of biofilms were significantly impacted by Cu, Mn, Zn, and salinity. Biofilms from the contaminated sites were dominated by tolerant taxa to contaminants and specialized hydrocarbon-degrading microorganisms. Functions related to major xenobiotics biodegradation and metabolism, such as methane metabolism, degradation of aromatic compounds, and benzoate degradation, as well as functions involved in quorum sensing signaling, extracellular polymeric substances (EPS) matrix, and biofilm formation were significantly over-represented in the contaminated site relative to the uncontaminated one. Taken together, our results suggest that biofilms may be able to survive to strong multi-chemical contamination because of the presence of tolerant taxa in biofilms, as well as the functional responses of biofilm communities. Moreover, biofilm communities exhibited significant variations of structure and functional profiles along the seawater column, potentially explained by the contribution of taxa from surrounding sediments. Finally, we found that both structure and functions were significantly distinct between the biofilm and bacterioplankton, highlighting major differences between the both lifestyles, and the divergence of their responses facing to a multi-chemical contamination.

Anthropogenic influence on the environmental health along Montenegro coast based on the bacterial and chemical characterization

Coastal marine sediments are particularly exposed to human activities. The function of a coastal ecosystem is largely affected by eutrophication, wastewater discharges, chemical pollution, port activities, industry and tourism. Bacterial classification can be used as a measure in assessing the harmful effects on the ecosystem. This study provided insight into the environmental health of the coastal region of Montenegro analyzing the possible impact of PAHs and PCBs upon the bacterial community diversity and function as well as nutrients. Two stations at the shipyards were defined as very high PAH polluted together with PCB concentration exceeding threshold values. The bacterial community at the OTU level clustered together all stations except the most polluted site (SBL), the main tourist destination in Montenegro (BDV) and the estuary site (ADB) forming the independent clusters. Bacterial community based on the OTU level was driven by PAHs, TOC and silt content. The lowest richness and diversity were indicated at the site with the highest concentration of PAHs and PCBs with the highest abundance of Alphaproteobacteria followed by Gammaproteobacteria. OTUs affiliated to phyla BRC1, Dadabacteria and Spirochaetes were present with a total abundance higher than 1% only at the most polluted site indicating their persistence and possible potential for degradation of aromatic compounds. To compare functional capabilities potentially related to biodegradation of aromatic compounds and active transport systems, PICRUSt was used to predict metagenomes of the sediments. From our data, we identified specific bacterial community and predicted metabolic pathways that give us a picture of the environmental health along the coast of Montenegro, which provides us a new insight into human-induced pollution impacts on the coastal ecosystem.

New evidence for a hydroxylation pathway for anaerobic alkane degradation supported by analyses of functional genes and signature metabolites in oil reservoirs

Microbial degradation of recalcitrant alkanes under anaerobic conditions results in the accumulation of heavy oil fraction in oil reservoirs. Hydroxylation of alkanes is an important activation mechanism under anaerobic conditions, but the diversity and distribution of the responsible microorganisms in the subsurface environment are still unclear. The lack of functional gene polymerase chain reaction (PCR) primers and commercially available intermediate degradation chemical compounds are the major obstacles for this research. In this investigation, PCR primers for the ahyA gene (encoding alkane hydroxylase) were designed, evaluated, and improved based on the nucleotide sequences available. Using microbial genomic DNA extracted from oil-contaminated soil and production water samples of oil reservoirs, ahyA gene nucleotide sequences were amplified and retrieved successfully from production water sample Z3-25 of Shengli oilfield. Additionally, the signature biomarker of 2-acetylalkanoic acid was detected in both Shengli and Jiangsu oilfields. These results demonstrate that anaerobic hydroxylation is an active mechanism used by microorganisms to degrade alkanes in oxygen-depleted oil reservoirs. This finding expands the current knowledge of biochemical reactions about alkane degradation in subsurface ecosystems. In addition, the PCR primers designed and tested in this study serve as an effective molecular tool for detecting the microorganisms responsible for anaerobic hydroxylation of alkanes in this and other ecosystems.

Taxonomic study of nine new Winogradskyella species occurring in the shallow waters of Helgoland Roads, North Sea. Proposal of Winogradskyella schleiferi sp. nov., Winogradskyella costae sp. nov., Winogradskyella helgolandensis sp. nov., Winogradskyella vidalii sp. nov., Winogradskyella forsetii sp. nov., Winogradskyella ludwigii sp. nov., Winogradskyella ursingii sp. nov., Winogradskyella wichelsiae sp. nov., and Candidatus "Winogradskyella atlantica" sp. nov

Evaluation of bacterial succession with cultivation-dependent strategies during a spring phytoplankton bloom in the North Sea led to the isolation of 41 strains that affiliated with the genus Winogradskyella. Fifteen of the strains were selected for a taxonomic study after discarding clonal cultures. A thorough phylogenetic, genomic and phenotypic analysis of the isolates indicated that they represented eight new species that coexisted in North Sea waters. Molecular data revealed the existence of an as yet uncultivated novel species recurrently binned from the North Sea metagenomes. The metagenome-assembled genomes (MAGs) of this new Winogradskyella were used to classify it as a new Candidatus species. This study represented a new example of the use of the tandem approach of whole cell mass spectrometry linked to 16S rRNA gene sequencing in order to facilitate the discovery of new taxa by high-throughput cultivation, which increases the probability of finding more than a single isolate for new species. In addition, we demonstrated the reasons for classifying MAGs representing recurrently retrieved heterotrophic species that evade cultivation even after an important high-throughput effort. The taxonomic study resulted in the classification of eight new species and one new Candidatus species of the genus Winogradskyella for which we propose the names W. schleiferi sp. nov., W. costae sp. nov., W. helgolandensis sp. nov., W. vidalii sp. nov., W. forsetii sp. nov., W. ludwigii sp. nov., W. ursingii sp. nov., W. wichelsiae sp. nov., and Candidatus "W. atlantica" sp. nov.

Understanding the role of bacterial cellular adsorption, accumulation and bioavailability regulation by biosurfactant in affecting biodegradation efficacy of polybrominated diphenyl ethers

Microbiological degradation is often considered as an important strategy to reduce the risks of polybrominated diphenyl ethers (PBDEs), which are environmentally widespread and harmful to human health and wildlife. With the well-identified aerobic bacteria, i.e. B. xenovorans LB400, the biodegradation of 2,2',4,4'-tetrabrominated diphenyl ether (BDE-47) occurred efficiently in conformity to the first-order kinetics and showed the strong dependence on initial concentration of pollutant and bioavailability regulation by biosurfactant. The mild increase of initial concentration of BDE-47 would enhance biodegradation whereas the excessive increase failed due to the oxidative stress or cytotoxicity to bacteria. Rather than the bacterial extracellular adsorption that was bioactively-mediated in thermodynamics, the intracellular accumulations at different time gradients showed the negative correlation with biodegradation efficiency of BDE-47. The spontaneous biodegradation of pollutant should be sourced from the gradual reduction of intracellular accumulation. Though the improved bioavailability of BDE-47 by sucrose fatty acid ester (SFAE) hardly altered the extracellular adsorption, the bacterial intracellular accumulation was indicated to increase continuously with used amount of biosurfactant and then decrease for the cellular morphological damage, and interestingly it appeared to be temporary reservoir for prompt delivery to biodegradation in light of the opposite variation tendency with time.

Functional potential and assembly of microbes from sediments in a lake bay and adjoining river ecosystem for polycyclic aromatic hydrocarbon biodegradation

Lake and adjoining river ecosystems are ecologically and economically valuable and are heavily threatened by anthropogenic activities. Determining the inherent capacity of ecosystems for polycyclic aromatic hydrocarbon (PAH) biodegradation can help quantify environmental impacts on the functioning of ecosystems, especially on that of the microbial community. Here, PAH biodegradation potential was compared between sediments collected from a lake bay (LS) and an adjoining river (RS) ecosystem. Microbial community composition, function, and their co-occurrence patterns were also explored. In the RS, the biodegradation rates (K_D ) of pyrene or PAH were almost two orders of magnitude higher than those in the LS. Sediment functional community structure and network interactions were dramatically different between the LS and RS. Although PAH degradation genes (p450aro, quinoline, and qorl) were detected in the LS, the community activity of these genes needed to be biostimulated for accelerated bioremediation. In contrast, functional communities in the RS were capable of spontaneous natural attenuation of PAH. The degradation of PAH in the RS also required coordinated response of the complex functional community. Taken together, elucidating functions and network interactions in sediment microbial communities and their responses to environmental changes are very important for the bioremediation of anthropogenic toxic contaminants.

Modelling Free-Living and Particle-Associated Bacterial Assemblages across the Deep and Hypoxic Lower St. Lawrence Estuary

The Estuary and Gulf of St. Lawrence (EGSL) in eastern Canada is an appealing ecosystem for studying how microbial communities and metabolic processes are related to environmental change. Ocean and climate variability result in large spatiotemporal variations in environmental conditions and oceanographic processes. The EGSL is also exposed to a variety of additional human pressures that threaten its integrity and sustainable use, including shipping, aquiculture, coastal development, and oil exploration. To monitor and perhaps mitigate the impacts of these human activities on the EGSL, a comprehensive understanding of the biological communities is required. In this study, we provide the first comprehensive view of bacterial diversity in the EGSL and describe the distinct bacterial assemblages associated with different environmental habitats. This work therefore provides an important baseline ecological framework for bacterial communities in the EGSL useful for further studies on how these communities may respond to environmental change.

The Estuary and Gulf of St. Lawrence (EGSL) in eastern Canada are among the largest and most productive coastal ecosystems in the world. Very little information on bacterial diversity exists, hampering our understanding of the relationships between bacterial community structure and biogeochemical function in the EGSL. During the productive spring period, we investigated free-living and particle-associated bacterial communities across the stratified waters of the Lower St. Lawrence Estuary, including the particle-rich surface and bottom boundary layers. Modelling of community structure based on 16S rRNA gene and transcript diversity identified bacterial assemblages specifically associated with four habitat types defined by water mass (upper water or lower water column) and size fraction (free living or particle associated). Assemblages from the upper waters represent sets of cooccurring bacterial populations that are widely distributed across Lower St. Lawrence Estuary surface waters and likely key contributors to organic matter degradation during the spring. In addition, we provide strong evidence that particles in deep hypoxic waters and the bottom boundary layer support a metabolically active bacterial community that is compositionally distinct from those of surface particles and the free-living communities. Among the distinctive features of the bacterial assemblage associated with lower-water particles was the presence of uncultivated lineages of Deltaproteobacteria, including marine myxobacteria. Overall, these results provide an important ecological framework for further investigations of the biogeochemical contributions of bacterial populations in this important coastal marine ecosystem.

IMPORTANCE The Estuary and Gulf of St. Lawrence (EGSL) in eastern Canada is an appealing ecosystem for studying how microbial communities and metabolic processes are related to environmental change. Ocean and climate variability result in large spatiotemporal variations in environmental conditions and oceanographic processes. The EGSL is also exposed to a variety of additional human pressures that threaten its integrity and sustainable use, including shipping, aquiculture, coastal development, and oil exploration. To monitor and perhaps mitigate the impacts of these human activities on the EGSL, a comprehensive understanding of the biological communities is required. In this study, we provide the first comprehensive view of bacterial diversity in the EGSL and describe the distinct bacterial assemblages associated with different environmental habitats. This work therefore provides an important baseline ecological framework for bacterial communities in the EGSL useful for further studies on how these communities may respond to environmental change.

Supervised machine learning is superior to indicator value inference in monitoring the environmental impacts of salmon aquaculture using eDNA metabarcodes

Increasing anthropogenic impact and global change effects on natural ecosystems has prompted the development of less expensive and more efficient bioassessments methodologies. One promising approach is the integration of DNA metabarcoding in environmental monitoring. A critical step in this process is the inference of ecological quality (EQ) status from identified molecular bioindicator signatures that mirror environmental classification based on standard macroinvertebrate surveys. The most promising approaches to infer EQ from biotic indices (BI) are supervised machine learning (SML) and the calculation of indicator values (IndVal). In this study we compared the performance of both approaches using DNA metabarcodes of bacteria and ciliates as bioindicators obtained from 152 samples collected from seven Norwegian salmon farms. Results from standard macroinvertebrate-monitoring of the same samples were used as reference to compare the accuracy of both approaches. First, SML outperformed the IndVal approach to infer EQ from eDNA metabarcodes. The Random Forest (RF) algorithm appeared to be less sensitive to noisy data (a typical feature of massive environmental sequence data sets) and uneven data coverage across EQ classes (a typical feature of environmental compliance monitoring scheme) compared to a widely used method to infer IndVals for the calculation of a BI. Second, bacteria allowed for a more accurate EQ assessment than ciliate eDNA metabarcodes. For the implementation of DNA metabarcoding into routine monitoring programmes to assess EQ around salmon aquaculture cages, we therefore recommend bacterial DNA metabarcodes in combination with SML to classify EQ categories based on molecular signatures.

Biogeochemical controls on biodegradation of buried oil along a coastal headland beach

Laboratory experiments investigated oxygen dynamics in buried oiled sands sampled from areas impacted by the Macondo spill. Measured oxygen fluxes in oil deposits that were permeable to tidal water ranged from 10^-3 to 10^-4 μmol/cm²-sec, orders of magnitude higher than fluxes in non-permeable deposits (10^-6 to 10^-7 μmol/cm²-sec). Oxygen dynamics were well described by 1-d models that represent increased oxygen consumption in oiled sands. Experiments demonstrated that when oxygen is present and the oil deposit is permeable to tidal water, biodegradation of alkylated phenanthrenes and dibenzothiophenes proceeded over time scales (i.e., weeks) to have a significant impact on the mass and quality of buried oil. For this biodegradation process to proceed, two independent conditions must be met, a source of oxygenated water has to be present (e.g., tidal flushing in the intertidal zone) and the oiled deposit has to be permeable to water (i.e., pores cannot be completely saturated with oil).

High Throughput Sediment DNA Sequencing Reveals Azo Dye Degrading Bacteria Inhabit Nearshore Sediments

Estuaries and coastal environments are often regarded as a critical resource for the bioremediation of organic pollutants such as azo dyes due to their high abundance and diversity of extremophiles. Bioremediation through the activities of azoreductase, laccase, and other associated enzymes plays a critical role in the removal of azo dyes in built and natural environments. However, little is known about the biodegradation genes and azo dye degradation genes residing in sediments from coastal and estuarine environments. In this study, high-throughput sequencing (16S rRNA) of sediment DNA was used to explore the distribution of azo-dye degrading bacteria and their functional genes in estuaries and coastal environments. Unlike laccase genes, azoreductase (azoR), and naphthalene degrading genes were ubiquitous in the coastal and estuarine environments. The relative abundances of most functional genes were higher in the summer compared to winter at locations proximal to the mouths of the Hanjiang River and its distributaries. These results suggested inland river discharges influenced the occurrence and abundance of azo dye degrading genes in the nearshore environments. Furthermore, the azoR genes had a significant negative relationship with total organic carbon, Hg, and Cr (p < 0.05). This study provides critical insights into the biodegradation potential of indigenous microbial communities in nearshore environments and the influence of environmental factors on microbial structure, composition, and function which is essential for the development of technologies for bioremediation in azo dye contaminated sites.

Anaerobic Microbial Degradation of Polycyclic Aromatic Hydrocarbons: A Comprehensive Review

Polycyclic aromatic hydrocarbons (PAHs) are a class of hazardous organic contaminants that are widely distributed in nature, and many of them are potentially toxic to humans and other living organisms. Biodegradation is the major route of detoxification and removal of PAHs from the environment. Aerobic biodegradation of PAHs has been the subject of extensive research; however, reports on anaerobic biodegradation of PAHs are so far limited. Microbial degradation of PAHs under anaerobic conditions is difficult because of the slow growth rate of anaerobes and low energy yield in the metabolic processes. Despite the limitations, some anaerobic bacteria degrade PAHs under nitrate-reducing, sulfate-reducing, iron-reducing, and methanogenic conditions. Anaerobic biodegradation, though relatively slow, is a significant process of natural attenuation of PAHs from the impacted anoxic environments such as sediments, subsurface soils, and aquifers. This review is intended to provide comprehensive details on microbial degradation of PAHs under various reducing conditions, to describe the degradation mechanisms, and to identify the areas that should receive due attention in further investigations.

Meta-16S rRNA Gene Phylogenetic Reconstruction Reveals the Astonishing Diversity of Cosmopolitan Myxobacteria

Numerous ecological studies on myxobacteria have been conducted, but their true diversity remains largely unknown. To bridge this gap, we implemented a comprehensive survey of diversity and distribution of myxobacteria by using 4997 publicly available 16S rRNA gene sequences (≥1200 bp) collected from several hundred sites across multiple countries and regions. In this study, the meta-16S rRNA gene phylogenetic reconstruction clearly revealed that these sequences could be classified into 998 species, 445 genera, 58 families, and 20 suborders, the great majority of which belonged to new taxa. Most cultured myxobacteria were strongly inclined to locate on the shallow branches of the phylogenetic tree; on the contrary, the majority of uncultured myxobacteria located on the deep branches. The geographical analysis of sequences based on their environmental categories clearly demonstrated that myxobacteria show a nearly cosmopolitan distribution, despite the presence of some habitat-specific taxa, especially at the genus and species levels. Among the abundant suborders, Suborder_4, Suborder_15, and Suborder_17 were more widely distributed in marine environments, while the remaining suborders preferred to reside in terrestrial ecosystems. In conclusion, this study profiles a clear framework of diversity and distribution of cosmopolitan myxobacteria and sheds light on the isolation of uncultured myxobacteria.

Biodegradation of petroleum hydrocarbons and changes in microbial community structure in sediment under nitrate-, ferric-, sulfate-reducing and methanogenic conditions

In the present study, the biodegradation behaviors of petroleum hydrocarbons under various reducing conditions were investigated. n-Alkanes and polycyclic aromatic hydrocarbons (PAHs) were degraded with NO₃^-, Fe³⁺, SO₄^2-, or HCO₃^- as terminal electron acceptors (TEAs), which link to four typical reducing conditions (i.e., nitrate-reducing, ferric-reducing, sulfate-reducing and methanogenic conditions, respectively) in sediment. The fastest degradation rates were achieved under sulfate-reducing conditions with half-lives of 49.51 days for n-alkanes and 58.74 days for PAHs. For short-chain n-alkanes and low-molecular weight (LMW) PAHs, relatively higher removal efficiencies were achieved under nitrate- and ferric-reducing conditions. The degradation of long-chain n-alkanes and high-molecular weight (HMW) PAHs coupled to methanogenesis was the most favored as compared with other reducing conditions. Carboxylation was found to be the principle mechanism for regulating n-alkane degradation coupled to denitrification, while the activation of n-alkanes by the addition of fumarate was the principle mechanism for the n-alkane degradation under sulfate-reducing conditions. The anaerobic metabolism of n-alkanes may not proceed via fumarate addition or carboxylation under ferric-reducing and methanogenic conditions. Illumina HiSeq sequencing revealed dissimilar structures of the microbial communities under various reducing conditions. It is hypothesized that the utilization of different TEAs for n-alkane and PAH degradation resulted in distinct microbial community structures, which were highly correlated with the varied degradation behaviors of petroleum hydrocarbons in sediment. The current results may provide reference value on better understanding the biodegradation behaviors of n-alkanes and PAHs in association with the induced microbial communities in sedimentary environments under the four typical reducing conditions.

Stimulation of indigenous microbes by optimizing the water cut in low permeability reservoirs for green and enhanced oil recovery

Low permeability oil reservoirs are a widespread petroleum reservoir type all over the world. Therefore, methods to recover these reservoirs efficiently are of importance to guarantee energy supply. Here we report our novel stimulation of indigenous microbes by optimizing the water cut in low permeability reservoirs for green and enhanced oil recovery. We aimed to investigate the characteristics of indigenous bacterial communities with changes in water cut in reservoirs by high-throughput sequencing technology, and reveal the mechanism and characteristics of the crude oil biotreatment under different crude oil-water ratio conditions and the optimum activation time of indigenous functional microbial groups in reservoirs. The indigenous microbial metabolism products were characterized by gas chromatography mass spectrometry. Results showed that Acinetobacter (47.1%) and Pseudomones (19.8%) were the main functional genus of crude oil degradation at the optimal activation time, and can reduce the viscosity of crude oil from 8.33 to 5.75 mPa·s. The dominant bacteria genus for oil recovery after activation of the production fluids was similar to those in the reservoirs with water cut of 60-80%. Furthermore seven mechanism pathways of enhancing oil recovery by the synergistic of functional microbial groups and their metabolites under different water cut conditions in low permeability reservoirs have been established.

Bacterial community assemblages in sediments under high anthropogenic pressure at Ichkeul Lake/Bizerte Lagoon hydrological system, Tunisia

Bacterial communities inhabiting sediments in coastal areas endure the effect of strong anthropogenic pressure characterized by the presence of multiple contaminants. Understanding the effect of pollutants on the organization of bacterial communities is of paramount importance in order to unravel bacterial assemblages colonizing specific ecological niches. Here, chemical and molecular approaches were combined to investigate the bacterial communities inhabiting the sediments of the Ichkeul Lake/Bizerte Lagoon, a hydrological system under anthropogenic pressure. Although the microbial community of the Ichkeul Lake sediment was different to that of the Bizerte Lagoon, common bacterial genera were identified suggesting a lake-lagoon continuum probably due to the hydrology of the system exchanging waters according to the season. These genera represent bacterial "generalists" maintaining probably general biogeochemical functions. Linear discriminant analysis effect size (LEfSe) showed significant differential abundance distribution of bacterial genera according to the habitat, the pollution type and level. Further, correlation analyses identified specific bacterial genera which abundance was linked with pesticides concentrations in the lake, while in the lagoon the abundance of specific bacterial genera was found linked with the concentrations of PAHs (Polycyclic aromatic hydrocarbons) and organic forms of Sn. As well, bacterial genera which abundance was not correlated with the concentrations of pollutants were identified in both lake and lagoon. These findings represent valuable information, pointing out specific bacterial genera associated with pollutants, which represent assets for developing bacterial tools for the implementation, the management, and monitoring of bioremediation processes to mitigate the effect of pollutants in aquatic ecosystems.

Degradation of 2,2',4,4'-tetrabromodiphenyl ether by Pycnoporus sanguineus in the presence of copper ions

The degradation of 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) by Pycnoporus sanguineus was investigated in order to explore the impact of the heavy metal Cu²⁺ on BDE-47 decomposition and the subsequent formation of metabolites, as well as to further elucidate the degradation mechanism of BDE-47. An increase in degradation rate from 18.63% to 49.76% in the first four days and its stabilization at (51.26 ± 0.08)% in the following days of BDE-47 incubation were observed. The presence of Cu²⁺ at 1 and 2 mg/L was found to promote the degradation rate to 56.41% and 60.79%, respectively, whereas higher level of Cu²⁺ (≥5 mg/L) inhibited the removal of BDE-47. The similar concentration effects of Cu²⁺ was also found on contents of fungal protein and amounts of metabolites. Both intracellular and extracellular enzymes played certain roles in BDE-47 transportation with the best degradation rate at 27.90% and 27.67% on the fourth and third day, individually. During the degradation of BDE-47, four types of hydroxylated polybrominated diphenyl ethers (OH-PBDEs), i.e., 6'-OH-BDE-47, 5'-OH-BDE-47, 4'-OH-BDE-17, 2'-OH-BDE-28, and two bromophenols, i.e., 2,4-DBP and 4-BP were detected and considered as degradation products. These metabolites were further removed by P. sanguineus at rates of 22.42%, 23.01%, 27.04%, 27.96%, 64.21%, and 40.62%, respectively.

Microbial metabolic strategies for overcoming low-oxygen in naturalized freshwater reservoirs surrounding the Athabasca Oil Sands: A proxy for End-Pit Lakes?

The success and sustainability of aquatic ecosystems are driven by the complex, cooperative metabolism of microbes. Ecological engineering strategies often strive to harness this syntrophic synergy of microbial metabolism for the reclamation of contaminated environments worldwide. Currently, there is a significant knowledge gap in our understanding of how the natural microbial ecology overcomes thermodynamic limitations in recovering contaminated environments. Here, we used in-situ metatranscriptomics and associated metataxonomic analyses on sediments collected from naturalized freshwater man-made reservoirs within the Athabasca Oil Sands region of Alberta, Canada. These reservoirs are unique since they are untouched by industrial mining processes and serve as representative endpoints for model landscape reconstruction. Results indicate that a microbial syntrophic cooperation has been established represented by the oxygenic and anoxygenic phototrophs, sustained through the efficient use of novel cellular mechanistic adaptations tailored to these unique thermodynamic conditions. Specifically, chemotaxis transcripts (cheY & MCPs-methyl-accepting chemotaxis proteins) were highly expressed, suggesting a highly active microbial response to gradients in environmental stimuli, resulting indirectly from hydrocarbon compound alteration. A high expression of photosynthetic activity, likely sustaining nutrient delivery to the similarly highly expressed methanogenic community acting in syntrophy during the breakdown of organics. Overall the more diversified functionality within sub-oxic sample locations indicates an ability to maintain efficient metabolism under thermodynamic constraints. This is the first study to holistically identify and characterize these types of in-situ, metabolic processes and address their thermodynamic feasibility within a global context for large landscape reconstruction. These characterizations of regional, natural landscapes surrounding the oil sands mining operation are severely lacking, but truly provide invaluable insight into end-point goals and targets for reclamation procedures.

Changes in Bacterioplankton Communities Resulting From Direct and Indirect Interactions With Trace Metal Gradients in an Urbanized Marine Coastal Area

Unraveling the relative importance of both environmental conditions and ecological processes regulating bacterioplankton communities is a central goal in microbial ecology. Marine coastal environments are among the most urbanized areas and as a consequence experience environmental pressures. The highly anthropized Toulon Bay (France) was considered as a model system to investigate shifts in bacterioplankton communities along natural and anthropogenic physicochemical gradients during a 1-month survey. In depth geochemical characterization mainly revealed strong and progressive Cd, Zn, Cu, and Pb contamination gradients between the entrance of the Bay and the north-western anthropized area. On the other hand, low-amplitude natural gradients were observed for other environmental variables. Using 16S rRNA gene sequencing, we observed strong spatial patterns in bacterioplankton taxonomic and predicted function structure along the chemical contamination gradient. Variation partitioning analysis demonstrated that multiple metallic contamination explained the largest part of the spatial biological variations observed, but DOC and salinity were also significant contributors. Network analysis revealed that biotic interactions were far more numerous than direct interactions between microbial groups and environmental variables. This suggests indirect effects of the environment, and especially trace metals, on the community through a few taxonomic groups. These spatial patterns were also partially found for predicted bacterioplankton functions, thus indicating a limited functional redundancy. All these results highlight both potential direct influences of trace metals contamination on coastal bacterioplankton and indirect forcing through biotic interactions and cascading.

Anaerobic degradation of hexadecane and phenanthrene coupled to sulfate reduction by enriched consortia from northern Gulf of Mexico seafloor sediment

To advance understanding of the fate of hydrocarbons released from the Deepwater Horizon oil spill and deposited in marine sediments, this study characterized the microbial populations capable of anaerobic hydrocarbon degradation coupled with sulfate reduction in non-seep sediments of the northern Gulf of Mexico. Anaerobic, sediment-free enrichment cultures were obtained with either hexadecane or phenanthrene as sole carbon source and sulfate as a terminal electron acceptor. Phylogenetic analysis revealed that enriched microbial populations differed by hydrocarbon substrate, with abundant SSU rRNA gene amplicon sequences from hexadecane cultures showing high sequence identity (up to 98%) to Desulfatibacillum alkenivorans (family Desulfobacteraceae), while phenanthrene-enriched populations were most closely related to Desulfatiglans spp. (up to 95% sequence identity; family Desulfarculaceae). Assuming complete oxidation to CO2, observed stoichiometric ratios closely resembled the theoretical ratios of 12.25:1 for hexadecane and 8.25:1 for phenanthrene degradation coupled to sulfate reduction. Phenanthrene carboxylic acid was detected in the phenanthrene-degrading enrichment cultures, providing evidence to indicate carboxylation as an activation mechanism for phenanthrene degradation. Metagenome-assembled genomes (MAGs) revealed that phenanthrene degradation is likely mediated by novel genera or families of sulfate-reducing bacteria along with their fermentative syntrophic partners, and candidate genes linked to the degradation of aromatic hydrocarbons were detected for future study.

Microbial diversity of two cold seep systems in gas hydrate-bearing sediments in the South China Sea

Cold seep is a unique habitat for microorganisms in deep marine sediments, and microbial communities and biogeochemical processes are still poorly understood, especially in relation to hydrate-bearing geo-systems. In this study, two cold seep systems were sampled and microbial diversity was studied at Site GMGS2-08 in the northern part of the South China Sea (SCS) during the GMGS2 gas hydrate expedition. The current cold seep system was composed of a sulfate methane transition zone (SMTZ) and an upper gas hydrate zone (UGHZ). The buried cold seep system was composed of an authigenic carbonate zone (ACZ) and a lower gas hydrate zone (LGHZ). These drill core samples provided an excellent opportunity for analyzing the microbial abundance and diversity based on quantitative polymerase chain reaction (qPCR) and high-throughput 16S rRNA gene sequencing. Compared to previous studies, the high relative abundance of ANME-1b, a clade of anaerobic methanotrophic archaea (ANME), may perform anaerobic oxidation of methane (AOM) in collaboration with ANME-2c and Desulfobacteraceae in the SMTZ, and the high relative abundances of Hadesarchaea, ANME-1b archaea and Aerophobetes bacteria were found in the gas hydrate zone (GHZ) at Site GMGS2-08. ANME-1b, detected in the GHZ, might mainly mediate the AOM process, and the process might occur in a wide depth range within the LGHZ. Moreover, bacterial communities were significantly different between the GHZ and non-GHZ sediments. In the ACZ, archaeal communities were different between the two samples from the upper and the lower layers, while bacterial communities shared similarities. Overall, this new record of cold seep microbial diversity at Site GMGS2-08 showed the complexity of the interaction between biogeochemical reactions and environmental conditions.

Microbial metal-sulfide oxidation in inactive hydrothermal vent chimneys suggested by metagenomic and metaproteomic analyses

Metal-sulfides are wide-spread in marine benthic habitats. At deep-sea hydrothermal vents, they occur as massive sulfide chimneys formed by mineral precipitation upon mixing of reduced vent fluids with cold oxygenated sea water. Although microorganisms inhabiting actively venting chimneys and utilizing compounds supplied by the venting fluids are well studied, only little is known about microorganisms inhabiting inactive chimneys. In this study, we combined 16S rRNA gene-based community profiling of sulfide chimneys from the Manus Basin (SW Pacific) with radiometric dating, metagenome (n = 4) and metaproteome (n = 1) analyses. Our results shed light on potential lifestyles of yet poorly characterized bacterial clades colonizing inactive chimneys. These include sulfate-reducing Nitrospirae and sulfide-oxidizing Gammaproteobacteria dominating most of the inactive chimney communities. Our phylogenetic analysis attributed the gammaproteobacterial clades to the recently described Woeseiaceae family and the SSr-clade found in marine sediments around the world. Metaproteomic data identified these Gammaproteobacteria as autotrophic sulfide-oxidizers potentially facilitating metal-sulfide dissolution via extracellular electron transfer. Considering the wide distribution of these gammaproteobacterial clades in marine environments such as hydrothermal vents and sediments, microbially accelerated neutrophilic mineral oxidation might be a globally relevant process in benthic element cycling and a considerable energy source for carbon fixation in marine benthic habitats.

Assessment of the bacterial community structure in shallow and deep sediments of the Perdido Fold Belt region in the Gulf of Mexico

The Mexican region of the Perdido Fold Belt (PFB), in northwestern Gulf of Mexico (GoM), is a geological province with important oil reservoirs that will be subjected to forthcoming oil exploration and extraction activities. To date, little is known about the native microbial communities of this region, and how these change relative to water depth. In this study we assessed the bacterial community structure of surficial sediments by high-throughput sequencing of the 16S rRNA gene at 11 sites in the PFB, along a water column depth gradient from 20 to 3,700 m, including five shallow (20–600 m) and six deep (2,800–3,700 m) samples. The results indicated that OTUs richness and diversity were higher for shallow sites (OTUs = 2,888.2 ± 567.88; H′ = 9.6 ± 0.85) than for deep sites (OTUs = 1,884.7 ± 464.2; H′ = 7.74 ± 1.02). Nonmetric multidimensional scaling (NMDS) ordination revealed that shallow microbial communities grouped separately from deep samples. Additionally, the shallow sites plotted further from each other on the NMDS whereas samples from the deeper sites (abyssal plains) plotted much more closely to each other. These differences were related to depth, redox potential, sulfur concentration, and grain size (lime and clay), based on the environmental variables fitted with the axis of the NMDS ordination. In addition, differential abundance analysis identified 147 OTUs with significant fold changes among the zones (107 from shallow and 40 from deep sites), which constituted 10 to 40% of the total relative abundances of the microbial communities. The most abundant OTUs with significant fold changes in shallow samples corresponded to Kordiimonadales, Rhodospirillales, Desulfobacterales (Desulfococcus), Syntrophobacterales and Nitrospirales (GOUTA 19, BD2-6, LCP-6), whilst Chromatiales, Oceanospirillales (Amphritea, Alcanivorax), Methylococcales, Flavobacteriales, Alteromonadales (Shewanella, ZD0117) and Rhodobacterales were the better represented taxa in deep samples. Several of the OTUs detected in both deep and shallow sites have been previously related to hydrocarbons consumption. Thus, this metabolism seems to be well represented in the studied sites, and it could abate future hydrocarbon contamination in this ecosystem. The results presented herein, along with biological and physicochemical data, constitute an available reference for further monitoring of the bacterial communities in this economically important region in the GoM.

Future Directions of Marine Myxobacterial Natural Product Discovery Inferred from Metagenomics

Over the last two decades, halophilic (organisms that thrive at high salt concentrations) and halotolerant (organisms that have adapted to high salt concentrations) myxobacteria emerged as an important source of structurally diverse secondary metabolites from the marine environment. This review explores the advance of metagenomics analysis and 16S rRNA gene phylogeny of the cultured and uncultured myxobacteria from marine and other salt-environments up to July 2018. The diversity of novel groups of myxobacteria in these environments appears unprecedented, especially in the Sorangiineae and Nannocystineae suborders. The Sandaracinaceae related clade in the Sorangiineae suborder seems more widely distributed compared to the exclusively marine myxobacterial cluster. Some of the previously identified clones from metagenomic studies were found to be related to the Nannocystineae suborder. This understanding provides the foundation for a vital, unexplored resource. Understanding the conditions required to cultivate these yet “uncultured” myxobacteria in the laboratory, while a key next step, offers a significant potential to further expand access to diverse secondary metabolites.

Ecological and molecular characterization of a coral black band disease outbreak in the Red Sea during a bleaching event

Black Band Disease (BBD) is a widely distributed and destructive coral disease that has been studied on a global scale, but baseline data on coral diseases is missing from many areas of the Arabian Seas. Here we report on the broad distribution and prevalence of BBD in the Red Sea in addition to documenting a bleaching-associated outbreak of BBD with subsequent microbial community characterization of BBD microbial mats at this reef site in the southern central Red Sea. Coral colonies with BBD were found at roughly a third of our 22 survey sites with an overall prevalence of 0.04%. Nine coral genera were infected including Astreopora, Coelastrea, Dipsastraea, Gardineroseris, Goniopora, Montipora, Pavona, Platygyra, and Psammocora. For a southern central Red Sea outbreak site, overall prevalence was 40 times higher than baseline (1.7%). Differential susceptibility to BBD was apparent among coral genera with Dipsastraea (prevalence 6.1%), having more diseased colonies than was expected based on its abundance within transects. Analysis of the microbial community associated with the BBD mat showed that it is dominated by a consortium of cyanobacteria and heterotrophic bacteria. We detected the three main indicators for BBD (filamentous cyanobacteria, sulfate-reducing bacteria (SRB), and sulfide-oxidizing bacteria (SOB)), with high similarity to BBD-associated microbes found worldwide. More specifically, the microbial consortium of BBD-diseased coral colonies in the Red Sea consisted of Oscillatoria sp. (cyanobacteria), Desulfovibrio sp. (SRB), and Arcobacter sp. (SOB). Given the similarity of associated bacteria worldwide, our data suggest that BBD represents a global coral disease with predictable etiology. Furthermore, we provide a baseline assessment of BBD disease prevalence in the Red Sea, a still understudied region.

Diversity and Dynamics of Microbial Community Structure in Different Mangrove, Marine and Freshwater Sediments During Anaerobic Debromination of PBDEs

Little is known about the diversity and succession of indigenous microbial community during debromination of polybrominated diphenyl ethers (PBDEs). This study examined the diversity and dynamics of microbial community structure in eight saline (mangrove and marine) and freshwater sediment microcosms exhibiting different debrominating capabilities for hexa-BDE 153, a common congener in sediments, using terminal restriction fragment length polymorphism (T-RFLP) and clone library analyses. The results showed that microbial community structure greatly differed between the saline and freshwater microcosms, likely leading to distinct variations in their debrominating capabilities and pathways. Higher relative abundances of Chloroflexi and Deltaproteobacteria succeed by Alphaproteobacteria and Betaproteobacteria were detected in the two mangrove microcosms with the fastest debrominating capabilities mainly via para pathway, respectively; the dominance of Alphaproteobacteria resulted in less accumulation of tetra-BDEs and more complete debromination of lower brominated congeners (from di- to tetra-BDEs). Meanwhile, the shifts in both microbial community structure and PBDE profiles were relatively small in the less efficient freshwater microcosms, with relatively more ortho and meta brominated products of BDE-153 resulted. Coincidently, one of the freshwater microcosms showed sudden increases of Chloroflexi and Deltaproteobacteria by the end of incubation, which synchronized with the increase in the removal rate of BDE-153. The significant relationship between microbial community structure and PBDEs was confirmed by redundancy analysis (18.7% of total variance explained, P = 0.002). However, the relative abundance of the well-known dechlorinator Dehalococcoides showed no clear correlation with the debrominating capability across different microcosms. These findings shed light in the significance of microbial community network in different saline environments on enhancement of PBDE intrinsic debromination.

Microbial diversity and ecotoxicity of sediments 3 years after the Jiaozhou Bay oil spill

In 2013, the “Qingdao oil pipeline explosion” released an estimated 2000 tons of oil into the environment. Sediment samples were collected from ten sites in Jiaozhou Bay and Shilaoren Beach to evaluate the influence of the spilled oil on the benthic environment 3 years after the oil spill accident. The compositions of oil, bacterial diversity and biotoxicity were examined in this study. The results showed that the concentration of total petroleum hydrocarbons (TPHs) peaked near the oil leak point and gradually decreased along the coastline, ranging from 21.5 to 133.2 μg/g. The distribution of polycyclic aromatic hydrocarbons (PAHs) was correlated with TPH, and naphthalenes were dominant in the 20 detected PAHs. The bacterial diversities in seriously polluted and slightly polluted sediments were completely different. As degrading bacteria, Alcanivorax and Lutibacter were the main genera at the oil-polluted sites. The analysis of biotoxicity by the luminescent bacteria method showed great differences among the polluted sites, the control site in Jiaozhou Bay, and the non-polluted site outside of Jiaozhou Bay. The biotoxicity also peaked at the site near the oil leak point. These results indicate that the oil spill that occurred 3 years ago still affects the environment and impacts the bacterial communities in the sediments.

Electrospun Gelatin Membrane Cross-Linked by a Bis(diarylcarbene) for Oil/Water Separation: A New Strategy To Prepare Porous Organic Polymers

Porous organic polymers (POPs) as absorbing materials have attracted increasing attention. Here, we report a new approach to prepare these polymers for selective oil absorption from oil/water mixtures. Perfluoroalkylbis(diaryldiazomethane) was synthesized and used to modify the surface of an electrospun gelatin membrane by a carbene insertion reaction, not only to immobilize the porous network morphology by cross-linking but also to introduce perfluoroalkyl groups for oil/water separation. The membrane was characterized to show its surface and bulk properties, as well as its performance for absorption capacity, selectivity, and renewability. This approach offers a new horizon in the preparation of POPs for oil/water separation.

Enhanced phenanthrene degradation in river sediments using a combination of biochar and nitrate

Polycyclic aromatic hydrocarbons (PAHs) pollution in urban river sediments is a serious problem to ecological systems and human health. We examined novel remediation approaches, using a biochar amendment combined with bioaugmentation or/and nitrate stimulation, to degrade phenanthrene in sediment. Biochar amendment combined with nitrate stimulation enhanced phenanthrene degradation by 2.3 times that of the control and 1.9 times that of biochar alone. Nitrate stimulation altered the microbial succession and encouraged the growth of potential nitrate-reducing PAH-degraders Thiobacillus and Stenotrophomonas. Biochar was an excellent sorbent for phenanthrene and the shelter that it provided PAH-degraders increased contact between phenanthrene and PAH-degraders. Biochar also enhanced the aging effects of phenanthrene and reduced the ecological risk by 7.7% to 11%. These results suggest that biochar amendment combined with nitrate stimulation can achieve high-efficiency phenanthrene degradation in sediments.

Metagenomic Analysis of Subtidal Sediments from Polar and Subpolar Coastal Environments Highlights the Relevance of Anaerobic Hydrocarbon Degradation Processes

In this work, we analyzed the community structure and metabolic potential of sediment microbial communities in high-latitude coastal environments subjected to low to moderate levels of chronic pollution. Subtidal sediments from four low-energy inlets located in polar and subpolar regions from both Hemispheres were analyzed using large-scale 16S rRNA gene and metagenomic sequencing. Communities showed high diversity (Shannon's index 6.8 to 10.2), with distinct phylogenetic structures (<40% shared taxa at the Phylum level among regions) but similar metabolic potential in terms of sequences assigned to KOs. Environmental factors (mainly salinity, temperature, and in less extent organic pollution) were drivers of both phylogenetic and functional traits. Bacterial taxa correlating with hydrocarbon pollution included families of anaerobic or facultative anaerobic lifestyle, such as Desulfuromonadaceae, Geobacteraceae, and Rhodocyclaceae. In accordance, biomarker genes for anaerobic hydrocarbon degradation (bamA, ebdA, bcrA, and bssA) were prevalent, only outnumbered by alkB, and their sequences were taxonomically binned to the same bacterial groups. BssA-assigned metagenomic sequences showed an extremely wide diversity distributed all along the phylogeny known for this gene, including bssA sensu stricto, nmsA, assA, and other clusters from poorly or not yet described variants. This work increases our understanding of microbial community patterns in cold coastal sediments, and highlights the relevance of anaerobic hydrocarbon degradation processes in subtidal environments.

Analysis of the bacterial microbiome in the small octopus, Octopus variabilis, from South Korea to detect the potential risk of foodborne illness and to improve product management

The small octopus (Octopus variabilis) is a popular seafood in many countries including South Korea. Because it is often consumed uncooked, the microorganisms in it often cause food poisoning. Therefore, analyzing the microbiome of the small octopus can help to understand the risk of food poisoning and manage octopus products better. A total of 40 small octopuses were collected from four sites in November and August. The microbiota was analyzed using Illumina Miseq sequencing, and the amount of bacteria was quantified by real-time PCR. In addition, we analyzed the influence of Vibrio vulnificus infection on the microbiome of the small octopus through artificial infection experiments. Bacteroidetes was the predominant phylum in August, and Proteobacteria was predominant in November. The composition of the microbiota in octopus depended on sampling region and season. The potential risk of foodborne illness from small octopus consumption might be higher in August than in November due to the abundance of potential pathogens. In the infection experiment, the proportion of V. vulnificus increased only at 27°C. The composition and functional gene profiles of the microbiota varied in a similar manner between non-infected and infected samples over time at the same temperature. These results indicated that the indigenous microbiota in small octopus could inhibit colonization by V. vulnificus during storage. Although further studies are necessary to clarify these results, our results could help us better understand food poisoning through octopus ingestion and manage products.

More than 2500 years of oil exposure shape sediment microbiomes with the potential for syntrophic degradation of hydrocarbons linked to methanogenesis

BACKGROUND

Natural oil seeps offer the opportunity to study the adaptation of ecosystems and the associated microbiota to long-term oil exposure. In the current study, we investigated a land-to-sea transition ecosystem called "Keri Lake" in Zakynthos Island, Greece. This ecosystem is unique due to asphalt oil springs found at several sites, a phenomenon already reported 2500 years ago. Sediment microbiomes at Keri Lake were studied, and their structure and functional potential were compared to other ecosystems with oil exposure histories of various time periods.

RESULTS

Replicate sediment cores (up to 3-m depth) were retrieved from one site exposed to oil as well as a non-exposed control site. Samples from three different depths were subjected to chemical analysis and metagenomic shotgun sequencing. At the oil-exposed site, we observed high amounts of asphalt oil compounds and a depletion of sulfate compared to the non-exposed control site. The numbers of reads assigned to genes involved in the anaerobic degradation of hydrocarbons were similar between the two sites. The numbers of denitrifiers and sulfate reducers were clearly lower in the samples from the oil-exposed site, while a higher abundance of methanogens was detected compared to the non-exposed site. Higher abundances of the genes of methanogenesis were also observed in the metagenomes from other ecosystems with a long history of oil exposure, compared to short-term exposed environments.

CONCLUSIONS

The analysis of Keri Lake metagenomes revealed that microbiomes in the oil-exposed sediment have a higher potential for methanogenesis over denitrification/sulfate reduction, compared to those in the non-exposed site. Comparison with metagenomes from various oil-impacted environments suggests that syntrophic interactions of hydrocarbon degraders with methanogens are favored in the ecosystems with a long-term presence of oil.

Naphthalene biodegradation under oxygen-limiting conditions: community dynamics and the relevance of biofilm-forming capacity

Toxic polycyclic aromatic hydrocarbons (PAHs) are frequently released into the environment from anthropogenic sources. PAH remediation strategies focus on biological processes mediated by bacteria. The availability of oxygen in polluted environments is often limited or absent, and only bacteria able to thrive in these conditions can be considered for bioremediation strategies. To identify bacterial strains able to degrade PAHs under oxygen‐limiting conditions, we set up enrichment cultures from samples of an oil‐polluted aquifer, using either anoxic or microaerophilic condition and with PAHs as the sole carbon source. Despite the presence of a significant community of nitrate‐reducing bacteria, the initial community, which was dominated by Betaproteobacteria, was incapable of PAH degradation under strict anoxic conditions, although a clear shift in the structure of the community towards an increase in the Alphaproteobacteria (Sphingomonadaceae), Actinobacteria and an uncultured group of Acidobacteria was observed in the enrichments. In contrast, growth under microaerophilic conditions with naphthalene as the carbon source evidenced the development of a biofilm structure around the naphthalene crystal. The enrichment process selected two co‐dominant groups which finally reached 97% of the bacterial communities: Variovorax spp. (54%, Betaproteobacteria) and Starkeya spp. (43%, Xanthobacteraceae). The two dominant populations were able to grow with naphthalene, although only Starkeya was able to reproduce the biofilm structure around the naphthalene crystal. The pathway for naphthalene degradation was identified, which included as essential steps dioxygenases with high affinity for oxygen, showing 99% identity with Xanthobacter polyaromaticivorans dbd cluster for PAH degradation. Our results suggest that the biofilm formation capacity of Starkeya provided a structure to allocate its cells at an appropriate distance from the toxic carbon source.

Building a bio-based industry in the Middle East through harnessing the potential of the Red Sea biodiversity

The incentive for developing microbial cell factories for production of fuels and chemicals comes from the ability of microbes to deliver these valuable compounds at a reduced cost and with a smaller environmental impact compared to the analogous chemical synthesis. Another crucial advantage of microbes is their great biological diversity, which offers a much larger "catalog" of molecules than the one obtainable by chemical synthesis. Adaptation to different environments is one of the important drives behind microbial diversity. We argue that the Red Sea, which is a rather unique marine niche, represents a remarkable source of biodiversity that can be geared towards economical and sustainable bioproduction processes in the local area and can be competitive in the international bio-based economy. Recent bioprospecting studies, conducted by the King Abdullah University of Science and Technology, have established important leads on the Red Sea biological potential, with newly isolated strains of Bacilli and Cyanobacteria. We argue that these two groups of local organisms are currently most promising in terms of developing cell factories, due to their ability to operate in saline conditions, thus reducing the cost of desalination and sterilization. The ability of Cyanobacteria to perform photosynthesis can be fully exploited in this particular environment with one of the highest levels of irradiation on the planet. We highlight the importance of new experimental and in silico methodologies needed to overcome the hurdles of developing efficient cell factories from the Red Sea isolates.

Microbial Community Response to Simulated Petroleum Seepage in Caspian Sea Sediments

Anaerobic microbial hydrocarbon degradation is a major biogeochemical process at marine seeps. Here we studied the response of the microbial community to petroleum seepage simulated for 190 days in a sediment core from the Caspian Sea using a sediment-oil-flow-through (SOFT) system. Untreated (without simulated petroleum seepage) and SOFT sediment microbial communities shared 43% bacterial genus-level 16S rRNA-based operational taxonomic units (OTU_0.945) but shared only 23% archaeal OTU_0.945. The community differed significantly between sediment layers. The detection of fourfold higher deltaproteobacterial cell numbers in SOFT than in untreated sediment at depths characterized by highest sulfate reduction rates and strongest decrease of gaseous and mid-chain alkane concentrations indicated a specific response of hydrocarbon-degrading Deltaproteobacteria. Based on an increase in specific CARD-FISH cell numbers, we suggest the following groups of sulfate-reducing bacteria to be likely responsible for the observed decrease in aliphatic and aromatic hydrocarbon concentration in SOFT sediments: clade SCA1 for propane and butane degradation, clade LCA2 for mid- to long-chain alkane degradation, clade Cyhx for cycloalkanes, pentane and hexane degradation, and relatives of Desulfobacula for toluene degradation. Highest numbers of archaea of the genus Methanosarcina were found in the methanogenic zone of the SOFT core where we detected preferential degradation of long-chain hydrocarbons. Sequencing of masD, a marker gene for alkane degradation encoding (1-methylalkyl)succinate synthase, revealed a low diversity in SOFT sediment with two abundant species-level MasD OTU_0.96.

Biodegradation of 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) by Phanerochaete chrysosporium in the presence of Cd2

Aerobic biodegradation of 2,2',4,4'-tetrabrominated diphenyl ether (BDE-47) by Phanerochaete chrysosporium in the presence of Cd²⁺ was investigated in this study. The results showed that P. chrysosporium could effectively degrade BDE-47, and its extracellular enzyme played an important role in the process of decomposition. BDE-47 biodegradation by fungi was more tolerant than extracellular enzyme in the presence of Cd²⁺. Also, both of the activity of two typical enzymes, MnP and LiP, descended with ascended Cd²⁺ concentration. Based on the four mono-hydroxylated PBDEs (5-OH-BDE-47, 4'-OH-BDE-17, 6-OH-BDE-47, and 2'-OH-BDE-28) and two bromophenols (2,4-DBP, 4-BP) detected, three possible degradation pathways were proposed, inferring that BDE-47 was more easily to transform via hydroxylation. With addition of Cd²⁺, the types of degradation products did not change, merely a variation of the content of these products observed. Meanwhile, the major metabolites of BDE-47, bromophenol compounds, have been found to be transformed or even mineralized by P. chrysosporium quickly, which also helped better explain why the amounts of BDE-47 decomposed did not match with that of the metabolites detected.

Permeability shapes bacterial communities in sublittoral surface sediments

The first interaction of water column-derived organic matter with benthic microbial communities takes place in surface sediments which are acting as biological filters catalyzing central steps of elemental cycling. Here we analyzed the bacterial diversity and community structure of sediment top layers at seven sites in the North Sea where sediment properties ranged from coarse-grained and highly permeable to fine-grained and impermeable. Bacterial communities in surface sediments were richer, more even and significantly different from communities in bottom waters as revealed by Illumina tag sequencing of 16S rRNA genes. Sediment permeability had a clear influence on community composition which was confirmed by CARD-FISH. Sulfate-reducing Desulfobacteraceae (2-5% of total cells), Flavobacteriaceae (3-5%) were more abundant in impermeable than in highly permeable sediments where acidobacterial Sva0725 dominated (11-15%). Myxobacterial Sandaracinaceae were most abundant in medium permeable sediments (3-7%). Woeseiaceae/JTB255 and Planctomycetes were major groups in all sediments (4-6%, 8-22%). Planctomycetes were highly diverse and branched throughout the phylum. We propose Planctomycetes as key bacteria for degradation of high molecular weight compounds and recalcitrant material entering surface sediments from the water column. Benthic Flavobacteriaceae likely have restricted capabilities for macromolecule degradation and might profit with Sandaracinaceae and Acidobacteria from low molecular weight compounds.