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In this study, we compared the genomes of three metal-resistant bacteria isolated from mercury-contaminated soil. We identified diverse and novel MGEs with evidence of multiple LGT events shaping their genomic structure and heavy metal resistance. Among the three metal-resistant strains, Sphingobium sp SA2 and Sphingopyxis sp SE2 were resistant to multiple metals including mercury, cadmium, copper, zinc and lead. Pseudoxanthomonas sp SE1 showed resistance to mercury only. Whole genome sequencing by Illumina and Oxford Nanopore technologies was undertaken to obtain comprehensive genomic data. The Sphingobium and Sphingopyxis strains contained multiple chromosomes and plasmids, whereas the Pseudoxanthomonas strain contained one circular chromosome. Consistent with their metal resistance profiles, the strains of Sphingobium and Sphingopyxis contained a higher quantity of diverse metal resistance genes across their chromosomes and plasmids compared to the single-metal resistant Pseudoxanthomonas SE1. In all three strains, metal resistance genes were principally associated with various novel MGEs including genomic islands (GIs), integrative conjugative elements (ICEs), transposons, insertion sequences (IS), recombinase in trio (RIT) elements and group II introns, indicating their importance in facilitating metal resistance adaptation in a contaminated environment. In the Pseudoxanthomonas strain, metal resistance regions were largely situated on a GI. The chromosomes of the strains of Sphingobium and Sphingopyxis contained multiple metal resistance regions, which were likely acquired by several GIs, ICEs, numerous IS elements, several Tn3 family transposons and RIT elements. Two of the plasmids of Sphingobium were impacted by Tn3 family transposons and ISs likely integrating metal resistance genes. The two plasmids of Sphingopyxis harboured transposons, IS elements, an RIT element and a group II intron. This study provides a comprehensive annotation of complex genomic re

The identification of tsunami deposits in the geological record remains a challenge because the proxies availabilities are subject to the environment. The proxies may degrade over time and inherently inhibit the robustness of event interpretations. Multi-proxy methods, which leverage on each other's advantage/s and limitation/s, are employed to improve the identification of tsunami deposits from the geological record. Here, we assess the utility of environmental DNA (eDNA) for tsunami research by comparing and contrasting the eDNA collected from a sequence of well-documented palaeotsunami deposits spanning the past three millennia. We study swales in a coastal beach ridge sequences on Phra Thong Island, Thailand and test if eDNA can robustly discriminate the tsunami-deposited sand sheets that intercalate between the non-tsunami derived organic mud layers. Our results indicate that the 2004 Indian Ocean tsunami deposit and preceding tsunami deposits (approximately 550 to 700 years ago) contain microbial communities that differ significantly from the overlying and underlying organic mud layers (p-value = 0.0269) but the signal becomes restricted in the older sediment layers up to 2800-year-old that are constantly submerged in groundwater. This work demonstrates the potential for applying eDNA to study tsunami deposits over centennial time frames and perhaps longer.

BACKGROUND: Metal corrosion in seawater has been extensively studied in surface and shallow waters. However, infrastructure is increasingly being installed in deep-sea environments, where extremes of temperature, salinity, and high hydrostatic pressure increase the costs and logistical challenges associated with monitoring corrosion. Moreover, there is currently only a rudimentary understanding of the role of microbially induced corrosion, which has rarely been studied in the deep-sea. We report here an integrative study of the biofilms growing on the surface of corroding mooring chain links that had been deployed for 10 years at ~2 km depth and developed a model of microbially induced corrosion based on flux-balance analysis. METHODS: We used optical emission spectrometry to analyze the chemical composition of the mooring chain and energy-dispersive X-ray spectrometry coupled with scanning electron microscopy to identify corrosion products and ultrastructural features. The taxonomic structure of the microbiome was determined using shotgun metagenomics and was confirmed by 16S amplicon analysis and quantitative PCR of the dsrB gene. The functional capacity was further analyzed by generating binned, genomic assemblies and performing flux-balance analysis on the metabolism of the dominant taxa. RESULTS: The surface of the chain links showed intensive and localized corrosion with structural features typical of microbially induced corrosion. The microbiome on the links differed considerably from that of the surrounding sediment, suggesting selection for specific metal-corroding biofilms dominated by sulfur-cycling bacteria. The core metabolism of the microbiome was reconstructed to generate a mechanistic model that combines biotic and abiotic corrosion. Based on this metabolic model, we propose that sulfate reduction and sulfur disproportionation might play key roles in deep-sea corrosion. CONCLUSIONS: The corrosion rate observed was higher than what could be expected f

AbstractSandy onshore deposits from tsunamis are difficult to distinguish from storm deposits, which makes it difficult to assess coastal hazards from the geological record. Here we analyse environmental DNA from microbial communities preserved in known tsunami and storm-deposited sediments and intercalating soils and non-marine sediments near Cuddalore, India, and Phra Thong Island, Thailand. Both sites were impacted by the 2004 Indian Ocean Tsunami and a subsequent storm flooding event (2011 Cyclone Thane at Cuddalore and a 2007 storm at Phra Thong Island). We show that the microbial communities in the overwash deposits are significantly different from soil and sediments that are not derived by overwash processes at both locations. Our method also successfully discriminates between modern tsunami deposits and storm deposits. We suggest molecular techniques have the potential to accurately discriminate overwash deposits from catastrophic natural events.

© 2019 Simoniello, Jencks, Lauro, Loftis, Weslawski, Deja, Forrest, Gossett, Jeffries, Jensen, Kobara, Nolan, Ostrowski, Pounds, Roseman, Basco, Gosselin, Reed, Wills and Wyatt. The democratization of ocean observation has the potential to add millions of observations every day. Though not a solution for all ocean monitoring needs, citizen scientists offer compelling examples showcasing their ability to augment and enhance traditional research and monitoring. Information they are providing is increasing the spatial and temporal frequency and duration of sampling, reducing time and labor costs for academic and government monitoring programs, providing hands-on STEM learning related to real-world issues and increasing public awareness and support for the scientific process. Examples provided here demonstrate the wide range of people who are already dramatically reducing gaps in our global observing network while at the same time providing unique opportunities to meaningfully engage in ocean observing and the research and conservation it supports. While there are still challenges to overcome before widespread inclusion in projects requiring scientific rigor, the growing organization of international citizen science associations is helping to reduce barriers. The case studies described support the idea that citizen scientists should be part of an effective global strategy for a sustained, multidisciplinary and integrated observing system.

We report the detection of volatile organic compound 1-cyclohexyl-2-pyrrolidone (CHP), in a bioelectrochemical system inoculated with Escherichia coli and supplemented with redox mediator 2-hydroxy-1,4-naphthoquinone (2-HNQ), using a functionalized carbon nanotube-coated screen-printed electrode (CNT-SPE) modified with –COOH and -NH2 functional groups. Addition of CHP decreased current output of the bioelectrochemical system, thus enabling rapid detection of CHP concentration. Under optimal conditions, the H2N-CNT-SPE was the best performing and a limit of detection (LOD) of 0.4 mg L−1 was achieved. The proposed sensor showed low interference from other inorganic and organic components. These results outline a viable strategy for detecting organic contaminants in environmental monitoring applications.

© 2017 by the authors; licensee MDPI, Basel, Switzerland. Organisms living in polar waters must cope with an extremely stressful environment dominated by freezing temperatures, high oxygen concentrations and UV radiation. To shed light on the genetic mechanisms on which the polar marine ciliate, Euplotes nobilii, relies to effectively cope with the oxidative stress, attention was focused on methionine sulfoxide reductases which repair proteins with oxidized methionines. A family of four structurally distinct MsrB genes, encoding enzymes specific for the reduction of the methionine-sulfoxide R-forms, were identified from a draft of the E. nobilii transcriptionally active (macronuclear) genome. The En-MsrB genes are constitutively expressed to synthesize proteins markedly different in amino acid sequence, number of CXXC motifs for zinc-ion binding, and presence/absence of a cysteine residue specific for the mechanism of enzyme regeneration. The En-MsrB proteins take different localizations in the nucleus, mitochondria, cytosol and endoplasmic reticulum, ensuring a pervasive protection of all the major subcellular compartments from the oxidative damage. These observations have suggested to regard the En-MsrB gene activity as playing a central role in the genetic mechanism that enables E. nobilii and ciliates in general to live in the polar environment.

© The Author 2017. As the cost of sequencing continues to fall, smaller groups increasingly initiate and manage larger sequencing projects and take on the complexity of data storage for high volumes of samples. This has created a need for low-cost laboratory information management systems (LIMS) that contain flexible fields to accommodate the unique nature of individual labs. Many labs do not have a dedicated information technology position, so LIMS must also be easy to setup and maintain with minimal technical proficiency. Findings: MetaLIMS is a free and open-source web-based application available via GitHub. The focus of MetaLIMS is to store sample metadata prior to sequencing and analysis pipelines. Initially designed for environmental metagenomics labs, in addition to storing generic sample collection information and DNA/RNA processing information, the user can also add fields specific to the user's lab. MetaLIMS can also produce a basic sequencing submission form compatible with the proprietary Clarity LIMS system used by some sequencing facilities. To help ease the technical burden associated with web deployment, MetaLIMS options the use of commercial web hosting combined with MetaLIMS bash scripts for ease of setup. Conclusions: MetaLIMS overcomes key challenges common in LIMS by giving labs access to a low-cost and open-source tool that also has the flexibility to meet individual lab needs and an option for easy deployment. By making the web application open source and hosting it on GitHub, we hope to encourage the community to build upon MetaLIMS, making it more robust and tailored to the needs of more researchers.

Elizabethkingia anophelis is an emerging pathogen that can cause life-threatening infections in neonates, severely immunocompromised and postoperative patients. The lack of genomic information on E. anophelis hinders our understanding of itsmechanisms of pathogenesis.Here,we report the first complete genomesequence of E. anophelisNUHP1 and assess its response to oxidative stress. Elizabethkingia anophelis NUHP1 has a circular genome of 4,369,828 base pairs and 4,141 predicted coding sequences. Sequence analysis indicates that E. anophelis has well-developed systems for scavenging iron and stress response. Many putative virulence factors and antibiotic resistance geneswere identified, underscoring potential host-pathogen interactions and antibiotic resistance. RNA-sequencing-based transcriptome profiling indicates that expressions of genes involved in synthesis of an yersiniabactin-like iron siderophore and heme utilization are highly induced as a protective mechanism toward oxidative stress caused by hydrogen peroxide treatment. Chromeazurol sulfonate assay verified that siderophore production of E. anophelis is increased in the presence of oxidative stress. We further showed that hemoglobin facilitates the growth, hydrogen peroxide tolerance, cell attachment, and biofilm formation of E. anophelis NUHP1. Our study suggests that siderophore production and heme uptake pathwaysmight play essential roles in stress response and virulence of the emerging pathogen E. anophelis.

In the era of metagenomics and amplicon sequencing comprehensive analyses of available sequence data remain a challenge. Here we describe an approach exploiting metagenomic and amplicon datasets from public databases to elucidate phylogenetic diversity of defined microbial taxa. We investigated the phylum Chlamydiae whose known members are obligate intracellular bacteria that represent important pathogens of humans and animals, as well as symbionts of protists. Despite their medical relevance, our knowledge about chlamydial diversity is still scarce. Most of the nine known families are represented by only a few isolates, while previous clone library based surveys suggested the existence of yet uncharacterized members of this phylum. Here we identified more than 22 000 high quality, non redundant chlamydial 16S rRNA gene sequences in diverse databases, as well as 1 900 putative chlamydial protein encoding genes. Even when applying the most conservative approach, clustering of chlamydial 16S rRNA gene sequences into operational taxonomic units revealed an unexpectedly high species, genus, and family-level diversity within the Chlamydiae, including 181 putative families. These in silico findings were verified experimentally in one Antarctic sample which contained a high diversity of novel Chlamydiae. In our analysis the Rhabdochlamydiaceae, whose known members infect arthropods, represents the most diverse and species-rich chlamydial family, followed by the protistassociated Parachlamydiaceae, and a putative new family (PCF8) with unknown host specificity. Available information on the origin of metagenomic samples indicated that marine environments contain the majority of the newly discovered chlamydial lineages, highlighting this environment as an important chlamydial reservoir.

Antarctica is arguably the world’s most important continent for influencing the Earth’s climate and ocean ecosystem function. The unique physico-chemical properties of the Southern Ocean enable high levels of microbial primary production to occur. This not only forms the base of a significant fraction of the global oceanic food web, but leads to the sequestration of anthropogenic CO2 and its transport to marine sediments, thereby removing it from the atmosphere; the Southern Ocean accounts for ~30% of global ocean uptake of CO2 despite representing ~10% of the total surface area of the global ocean.The Antarctic continent itself harbors some liquid water, including a remarkably diverse range of surface and subglacial lakes. Being one of the remaining natural frontiers, Antarctica delivers the paradox of needing to be protected from disturbance while requiring scientific endeavour to discover what is indigenous and learn how best to protect it. Moreover, like many natural environments on Earth, in Antarctica microorganisms dominate the genetic pool and biomass of the colonizable niches and play the key roles in maintaining proper ecosystem function. This review puts into perspective insight that has been and can be gained about Antarctica’s aquatic microbiota by using molecular biology, and in particular, metagenomic approaches.

We performed a metagenomic survey (6.6 Gbp of 454 sequence data) of Southern Ocean (SO) microorganisms during the austral summer of 2007–2008, examining the genomic signatures of communities across a latitudinal transect from Hobart (44°S) to the Mertz Glacier, Antarctica (67°S). Operational taxonomic units (OTUs) of the SAR11 and SAR116 clades and the cyanobacterial genera Prochlorococcus and Synechococcus were strongly overrepresented north of the Polar Front (PF). Conversely, OTUs of the Gammaproteobacterial Sulfur Oxidizer-EOSA-1 (GSO-EOSA-1) complex, the phyla Bacteroidetes and Verrucomicrobia and order Rhodobacterales were characteristic of waters south of the PF. Functions enriched south of the PF included a range of transporters, sulphur reduction and histidine degradation to glutamate, while branched-chain amino acid transport, nucleic acid biosynthesis and methionine salvage were overrepresented north of the PF. The taxonomic and functional characteristics suggested a shift of primary production from cyanobacteria in the north to eukaryotic phytoplankton in the south, and reflected the different trophic statuses of the two regions. The study provides a new level of understanding about SO microbial communities, describing the contrasting taxonomic and functional characteristics of microbial assemblages either side of the PF.

Psychrophilic (cold-adapted) microorganisms make a major contribution to the Earth’s biomass and perform critical roles in global biogeochemical cycles. The vast extent and environmental diversity of Earth’s cold biosphere has selected for equally diverse microbial assemblages that can include archaea, bacteria, eucarya and viruses. Molecular biology-based studies, and particularly DNA sequencing of whole environmental samples (metagenomics), has not only revealed the diversity of psychrophilic taxa, but revealed a capacity to perform a broad range of functions and microbial processes. Underpinning the important ecological roles of psychrophiles are exquisite mechanisms of physiological adaptation, involving specific cellular components (e.g. lipid membranes), genomic traits and patterns of global gene expression. Evolution has also selected for cold-active traits at the level of molecular adaptation, and enzymes from psychrophiles are characterized by specific structural, functional and stability properties. These characteristics of enzymes from psychrophiles not only manifest in efficient low temperature activity, but result in a flexible protein structure that enables biocatalysis in non-aqueous solvents, and provides the basis for significant enhancement of catalytic performance under a wide range of challenging conditions. In this review we examine the ecology of Antarctic psychrophiles, physiological adaptation of psychrophiles, and properties of cold-adapted proteins, and provide a view of how these characteristics inform studies of astrobiology.

Planktonic bacteria dominate surface ocean biomass and influence global biogeochemical processes, but remain poorly characterized, due to difficulties in cultivation.By employing large-scale single cell genomics, we obtained the first insights into the genome content and biogeography of many bacterial lineages inhabiting the surface ocean. We found that, compared to existing cultures, natural bacterioplankton have smaller genomes, fewer gene duplications, and are depleted in GC, non-coding nucleotides, and genes encoding transcription, signal transduction, and non-cytoplasmic proteins. This provides strong evidence that genome streamlining and oligotrophy are prevalent features among diverse, freeliving bacterioplankton, while existing laboratory cultures consist primarily of copiotrophs. The apparent ubiquity of metabolic specialization and mixotrophy, as predicted from single cell genomes, may also contribute to the difficulty in bacterioplankton cultivation. By employing metagenome fragment recruitment against single cell genomes, we show that the global distribution of surface ocean bacterioplankton correlates with temperature and latitude and is not limited by dispersal at time scales that are required for nucleotide substitution to exceed the current operational definition of bacterial species. Single cell genomes with highly similar SSU rRNA gene sequences exhibited significant biogeographic variability, highlighting challenges in the interpretation of individual gene surveys and metagenome assemblies in environmental microbiology. Our study demonstrates the utility of single cell genomics towards an improved understanding of the composition and dynamics of natural microbial assemblages.

Organic Lake is a shallow, marine-derived hypersaline lake in the Vestfold Hills, Antarctica that has the highest reported concentration of dimethylsulfide (DMS) in a natural body of water. To determine the composition and functional potential of the microbial community and learn about the unusual sulfur chemistry in Organic Lake, shotgun metagenomics was performed on size-fractionated samples collected along a depth profile. Eucaryal phytoflagellates were the main photosynthetic organisms. Bacteria were dominated by the globally distributed heterotrophic taxa Marinobacter, Roseovarius and Psychroflexus. The dominance of heterotrophic degradation, coupled with low fixation potential, indicates possible net carbon loss. However, abundant marker genes for aerobic anoxygenic phototrophy, sulfur oxidation, rhodopsins and CO oxidation were also linked to the dominant heterotrophic bacteria and indicate use of photo- and lithoheterotrophy as mechanisms for conserving organic carbon. Similarly, a high genetic potential for the recycling of nitrogen compounds likely functions to retain fixed nitrogen in the lake. Dimethylsulfoniopropionate (DMSP) lyase genes were abundant indicating DMSP is a significant carbon and energy source. Unlike marine environments, DMSP demethylases were less abundant, indicating that DMSP cleavage is the likely source of the high DMS concentration. DMSP cleavage, carbon mixotrophy (photoheterotrophy and lithoheterotrophy) and nitrogen remineralization by dominant Organic Lake bacteria are potentially important adaptations to nutrient constraints. In particular, carbon mixotrophy relieves the extent of carbon oxidation for energy production, allowing more carbon to be used for biosynthetic processes. The study sheds light on how the microbial community has adapted to this unique Antarctic lake environment.

While environmental selection and spatial separation have been shown to shape the distribution and abundance of marine microorganisms, the effects of advection (physical transport) have not been directly tested. Here we examine 25 samples covering all major water masses of the Southern Ocean to determine the effects of advection on microbial biogeography. Even when environmental factors and spatial separation are controlled for, there is a positive correlation between advection distance and taxonomic dissimilarity, indicating that an "advection effect" plays a role in shaping marine microbial community composition. This effect is likely due to the advection of cells increasing the probability that upstream microorganisms will colonise downstream sites. Our study shows that in addition to distance and environmental selection, advection shapes the composition of marine microbial communities.

Deep Lake in Antarctica is a globally isolated, hypersaline system that remains liquid at temperatures down to -20 °C. By analyzing metagenome data and genomes of four isolates we assessed genome variation and patterns of gene exchange to learn how the lake community evolved. The lake is completely and uniformly dominated by haloarchaea, comprising a hierarchically structured, low-complexity community that differs greatly to temperate and tropical hypersaline environments. The four Deep Lake isolates represent distinct genera (~85% 16S rRNA gene similarity and ~73% genome average nucleotide identity) with genomic characteristics indicative of niche adaptation, and collectively account for ~72% of the cellular community. Network analysis revealed a remarkable level of intergenera gene exchange, including the sharing of long contiguous regions (up to 35 kb) of high identity (~100%). Although the genomes of closely related Halobacterium, Haloquadratum, and Haloarcula (>90% average nucleotide identity) shared regions of high identity between species or strains, the four Deep Lake isolates were the only distantly related haloarchaea to share long high-identity regions. Moreover, the Deep Lake high-identity regions did not match to any other hypersaline environment metagenome data. The most abundant species, tADL, appears to play a central role in the exchange of insertion sequences, but not the exchange of high-identity regions. The genomic characteristics of the four haloarchaea are consistent with a lake ecosystem that sustains a high level of intergenera gene exchange while selecting for ecotypes that maintain sympatric speciation. The peculiarities of this polar system restrict which species can grow and provide a tempo and mode for accentuating gene exchange.

The ubiquitous SAR11 bacterial clade is the most abundant type of organism in the world's oceans, but the reasons for its success are not fully elucidated. We analysed 128 surface marine metagenomes, including 37 new Antarctic metagenomes. The large size of the dataset enabled internal transcribed spacer (ITS) regions to be obtained from the Southern polar region, enabling the first global characterisation of the distribution of SAR11, from waters spanning temperatures -2ºC to 30ºC. Our data show a stable co-occurrence of phylotypes within both "tropical" (>20ºC) and "polar" (

SHAP (simple high-throughput annotation pipeline) is a lightweight and scalable sequence annotation pipeline capable of supporting research efforts that generate or utilize large volumes of DNA sequence data. The software provides Grid capable analysis, relational storage and Web-based full-text searching of annotation results. Implemented in Java, SHAP recognizes the limited resources of many smaller research groups. © The Author 2011. Published by Oxford University Press. All rights reserved.

es are abundant ubiquitous members of microbial communities and in the marine environment affect population structure and nutrient cycling by infecting and lysing primary producers. Antarctic lakes are microbially dominated ecosystems supporting truncated food webs in which viruses exert a major influence on the microbial loop. Here we report the discovery of a virophage (relative of the recently described Sputnik virophage) that preys on phycodnaviruses that infect prasinophytes (phototrophic algae). By performing metaproteogenomic analysis on samples from Organic Lake, a hypersaline meromictic lake in Antarctica, complete virophage and near-complete phycodnavirus genomes were obtained. By introducing the virophage as an additional predator of a predator-prey dynamic model we determined that the virophage stimulates secondary production through the microbial loop by reducing overall mortality of the host and increasing the frequency of blooms during polar summer light periods. Virophages remained abundant in the lake 2 y later and were represented by populations with a high level of major capsid protein sequence variation (25-100% identity). Virophage signatures were also found in neighboring Ace Lake (in abundance) and in two tropical lakes (hypersaline and fresh), an estuary, and an ocean upwelling site. These findings indicate that virophages regulate host-virus interactions, influence overall carbon flux in Organic Lake, and play previously unrecognized roles in diverse aquatic ecosystems.

In nature, the complexity and structure of microbial communities varies widely, ranging from a few species to thousands of species, and from highly structured to highly unstructured communities. Here, we describe the identity and functional capacity of microbial populations within distinct layers of a pristine, marine-derived, meromictic (stratified) lake (Ace Lake) in Antarctica. Nine million open reading frames were analyzed, representing microbial samples taken from six depths of the lake size fractionated on sequential 3.0, 0.8 and 0.1 m filters, and including metaproteome data from matching 0.1 m filters. We determine how the interactions of members of this highly structured and moderately complex community define the biogeochemical fluxes throughout the entire lake. Our view is that the health of this delicate ecosystem is dictated by the effects of the polar light cycle on the dominant role of green sulfur bacteria in primary production and nutrient cycling, and the influence of viruses/phage and phage resistance on the cooperation between members of the microbial community right throughout the lake. To test our assertions, and develop a framework applicable to other microbially driven ecosystems, we developed a mathematical model that describes how cooperation within a microbial system is impacted by periodic fluctuations in environmental parameters on key populations of microorganisms. Our study reveals a mutualistic structure within the microbial community throughout the lake that has arisen as the result of mechanistic interactions between the physico-chemical parameters and the selection of individual members of the community. By exhaustively describing and modelling interactions in Ace Lake, we have developed an approach that may be applicable to learning how environmental perturbations affect the microbial dynamics in more complex aquatic systems. © 2011 International Society for Microbial Ecology All rights reserved.