Arsenic and selenium are readily metabolized by prokaryotes, participating in a full range of metabolic functions including assimilation, methylation, detoxification, and anaerobic respiration. Arsenic speciation and mobility is affected by microbes through oxidation/reduction reactions as part of resistance and respiratory processes. A robust arsenic cycle has been demonstrated in diverse environments. Respiratory arsenate reductases, arsenic methyltransferases, and new components in arsenic resistance have been recently described. The requirement for selenium stems primarily from its incorporation into selenocysteine and its function in selenoenzymes. Selenium oxyanions can serve as an electron acceptor in anaerobic respiration, forming distinct nanoparticles of elemental selenium that may be enriched in (76)Se. The biogenesis of selenoproteins has been elucidated, and selenium methyltransferases and a respiratory selenate reductase have also been described. This review highlights recent advances in ecology, biochemistry, and molecular biology and provides a prelude to the impact of genomics studies.

Bacteriophages typically have small genomes 1 and depend on their bacterial hosts for replication 2 . Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is-to our knowledge-the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undescribed CRISPR-Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins. The CRISPR-Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phages may repurpose bacterial CRISPR-Cas systems to eliminate competing phages. We phylogenetically define the major clades of huge phages from human and other animal microbiomes, as well as from oceans, lakes, sediments, soils and the built environment. We conclude that the large gene inventories of huge phages reflect a conserved biological strategy, and that the phages are distributed across a broad bacterial host range and across Earth's ecosystems.Phages-viruses that infect bacteria-are considered distinct from cellular life owing to their inability to carry out most biological processes required for reproduction. They are agents of ecosystem change because they prey on specific bacterial populations, mediate lateral gene transfer, alter host metabolism and redistribute bacterially derived compounds through cell lysis 2-4 . They spread antibiotic resistance 5 and disperse pathogenicity factors that cause disease in humans and animals 6,7 . Most knowledge about phages is based on laboratorystudied examples, the vast majority of which have genomes that are a few tens of kb in length. Widely used isolation-based methods select against large phage particles, and they can be excluded from phage concentrates obtained by passage through 100-nm or 200-nm filters 1 . In 2017, only 93 isolated phages with genomes that were more than 200 kb in length were published 1 . Sequencing of whole-community DNA can uncover phage-derived fragments; however, large genomes can still escape detection owing to fragmentation 8 . A new clade of human-and animal-associated megaphages was recently described on the basis of genomes that were manually curated to completion from metagenomic datasets 9 . This finding prompted us to carry out a more-comprehensive analysis of microbial communities to evaluate the prevalence, diversity and ecosystem distribution of phages with large genomes. Previously, phages with genomes of more than 200 kb have been referred to as 'jumbophages' 1 or, in the case of phages with genomes of more than 500 kb, as megaphages 9 . As the set reconstructed here span both size ranges we refer to them simply as 'huge phage...

A previously unknown chemolithoautotrophic arsenite-oxidizing bacterium has been isolated from a gold mine in the Northern Territory of Australia. The organism, designated NT-26, was found to be a gram-negative motile rod with two subterminal flagella. In a minimal medium containing only arsenite as the electron donor (5 mM), oxygen as the electron acceptor, and carbon dioxide-bicarbonate as the carbon source, the doubling time for chemolithoautotrophic growth was 7.6 h. Arsenite oxidation was found to be catalyzed by a periplasmic arsenite oxidase (optimum pH, 5.5). Based upon 16S rDNA phylogenetic sequence analysis, NT-26 belongs to the Agrobacterium/Rhizobium branch of the ␣-Proteobacteria and may represent a new species. This recently discovered organism is the most rapidly growing chemolithoautotrophic arsenite oxidizer known.Arsenic is found in many environments and is toxic to life in some forms. When present in insoluble forms, which are nontoxic, arsenic is frequently found as a mineral in combination with sulfur (e.g., orpiment [As 2 S 3 ] and realgar [AsS]) and especially with iron and sulfur (e.g., arsenopyrite [FeAsS]). The oxidation of these insoluble forms, chemically and/or microbiologically, results in the formation of arsenite (As III [H 3 AsO 3 ]). In environments such as acid mine drainage, arsenite concentrations can be extremely high (2 to 13 mg/liter) (22). The arsenite formed in various environments can then be oxidized to arsenate (As V [H 2 AsO 4 Ϫ ϩ H ϩ ]). Both of these soluble forms of arsenic, arsenite and arsenate, are toxic to living organisms, with arsenite considered more toxic than arsenate (5, 22).Interestingly, the chemical oxidation of arsenite to arsenate is slow. Most arsenite is, therefore, oxidized to arsenate microbiologically (22). Arsenite-oxidizing bacteria were first described in 1918 (7). These organisms, as well as a number of others that have been isolated more recently, are almost all heterotrophic arsenite-oxidizing bacteria, as they require the presence of organic matter for growth (17,18,23,24). The most common organism found has been Alcaligenes faecalis (7,17,18,23,24). For these heterotrophic bacteria, the oxidation (equation 1) is considered a detoxification mechanism rather than one that can support growth, despite the fact that the reaction is exergonic.Only one bacterium has been described that is able to use the energy gained from this reaction for growth. This organism, Pseudomonas arsenitoxidans, was found to grow chemolithoautotrophically with arsenite, oxygen, and carbon dioxide. The fastest doubling time reported for growth with arsenite was, however, in the order of 2 days (8). This report describes a new bacterium, isolated from a gold mine in the Northern Territory of Australia, that can also grow chemolithoautotrophically with arsenite as the electron donor, oxygen as the electron acceptor, and carbon dioxide (CO 2 ) or bicarbonate (HCO 3 Ϫ ) as the carbon source. Growth was rapid, with a doubling time of 7.6 h for chemolithoautotrophic grow...

Bacteriophages (phages) dramatically shape microbial community composition, redistribute nutrients via host lysis and drive evolution through horizontal gene transfer. Despite their importance, much remains to be learned about phages in the human microbiome. We investigated the gut microbiomes of humans from Bangladesh and Tanzania, two African baboon social groups and Danish pigs; many of these microbiomes contain phages belonging to a clade with genomes >540 kilobases in length, the largest yet reported in the human microbiome and close to the maximum size ever reported for phages. We refer to these as Lak phages. CRISPR spacer targeting indicates that Lak phages infect bacteria of the genus Prevotella. We manually curated to completion 15 distinct Lak phage genomes recovered from metagenomes. The genomes display several interesting features, including use of an alternative genetic code, large intergenic regions that are highly expressed and up to 35 putative transfer RNAs, some of which contain enigmatic introns. Different individuals have distinct phage genotypes, and shifts in variant frequencies over consecutive sampling days reflect changes in the relative abundance of phage subpopulations. Recent homologous recombination has resulted in extensive genome admixture of nine baboon Lak phage populations. We infer that Lak phages are widespread in gut communities that contain the Prevotella species, and conclude that megaphages, with fascinating and underexplored biology, may be common but largely overlooked components of human and animal gut microbiomes.

Arsenite [As(III)]-enriched anoxic bottom water from Mono Lake, California, produced arsenate [As(V)] during incubation with either nitrate or nitrite. No such oxidation occurred in killed controls or in live samples incubated without added nitrate or nitrite. A small amount of biological As(III) oxidation was observed in samples amended with Fe(III) chelated with nitrolotriacetic acid, although some chemical oxidation was also evident in killed controls. A pure culture, strain MLHE-1, that was capable of growth with As(III) as its electron donor and nitrate as its electron acceptor was isolated in a defined mineral salts medium. Cells were also able to grow in nitrate-mineral salts medium by using H 2 or sulfide as their electron donor in lieu of As(III). Arsenite-grown cells demonstrated dark 14 CO 2 fixation, and PCR was used to indicate the presence of a gene encoding ribulose-1,5-biphosphate carboxylase/oxygenase. Strain MLHE-1 is a facultative chemoautotroph, able to grow with these inorganic electron donors and nitrate as its electron acceptor, but heterotrophic growth on acetate was also observed under both aerobic and anaerobic (nitrate) conditions. Phylogenetic analysis of its 16S ribosomal DNA sequence placed strain MLHE-1 within the haloalkaliphilic Ectothiorhodospira of the ␥-Proteobacteria. Arsenite oxidation has never been reported for any members of this subgroup of the Proteobacteria.Arsenic (As) is a known carcinogen in drinking water, occurring therein primarily as arsenate [As(V)] or as arsenite [As(III)], with the latter oxyanion having greater toxicity and hydrologic mobility than the former (10). Although various chemical agents can drive the redox reactions occurring between the As(V) and As(III) species (7, 31), it has been shown that specific microbiological detoxification mechanisms can achieve this as well (5, 30). Recent discoveries have revealed that the biochemical reduction or oxidation of these two inorganic As species can also be coupled with energy conservation in some prokaryotes. Thus, respiratory (dissimilatory) reduction of As(V) is found in several phylogenetically diverse anaerobic Bacteria and Crenarchaeota (28), while the aerobic oxidation of As(III) provides energy for the rapid growth of chemoautotrophic bacteria isolated from gold mines (34, 35).Significant lithotrophic oxidative processes need not necessarily be coupled biochemically with oxygen. Such reactions can occur under anoxic conditions, provided that the oxidant has a higher electrochemical potential than the reductant. Examples of this phenomenon are the bacterial oxidation of Fe(II) with nitrate (44) and the oxidation of phosphite by sulfate reducers (36). Here we explore the potential of oxidants such as nitrate and Fe(III) to be coupled with the microbial oxidation of As(III) to As(V).Arsenic-rich Mono Lake, California, was selected as the source of materials for investigation. The high content of dissolved inorganic arsenic (200 M) in this stratified soda lake (pH 9.8; salinity, 70 to 90 g liter Ϫ1 ) i...

Arsenate [As(V)]-respiring bacteria affect the speciation and mobilization of arsenic in the environment. This can lead to arsenic contamination of drinking water supplies and deleterious consequences for human health. Using molecular genetics, we show that the functional gene for As(V) respiration, arrA, is highly conserved; that it is required for As(V) reduction to arsenite when arsenic is sorbed onto iron minerals; and that it can be used to identify the presence and activity of As(V)-respiring bacteria in arsenic-contaminated iron-rich sediments. The expression of arrA thus can be used to monitor sites in which As(V)-respiring bacteria may be controlling arsenic geochemistry.

SummaryConjugative pili are widespread bacterial appendages that play important roles in horizontal gene transfer, in spread of antibiotic resistance genes, and as sites of phage attachment. Among conjugative pili, the F “sex” pilus encoded by the F plasmid is the best functionally characterized, and it is also historically the most important, as the discovery of F-plasmid-mediated conjugation ushered in the era of molecular biology and genetics. Yet, its structure is unknown. Here, we present atomic models of two F family pili, the F and pED208 pili, generated from cryoelectron microscopy reconstructions at 5.0 and 3.6 Å resolution, respectively. These structures reveal that conjugative pili are assemblies of stoichiometric protein-phospholipid units. We further demonstrate that each pilus type binds preferentially to particular phospholipids. These structures provide the molecular basis for F pilus assembly and also shed light on the remarkable properties of conjugative pili in bacterial secretion and phage infection.

The arsenic (As) drinking water crisis in south and south-east Asia has stimulated intense study of the microbial processes controlling the redox cycling of As in soil-water systems. Microbial oxidation of arsenite is a critical link in the global As cycle, and phylogenetically diverse arsenite-oxidizing microorganisms have been isolated from various aquatic and soil environments. However, despite progress characterizing the metabolism of As in various pure cultures, no functional gene approaches have been developed to determine the importance and distribution of arsenite-oxidizing genes in soil-water-sediment systems. Here we report for the first time the successful amplification of arsenite oxidase-like genes (aroA/asoA/aoxB) from a variety of soil-sediment and geothermal environments where arsenite is known to be oxidized. Prior to the current work, only 16 aroA/asoA/aoxB-like gene sequences were available in GenBank, most of these being putative assignments from homology searches of whole genomes. Although aroA/asoA/aoxB gene sequences are not highly conserved across disparate phyla, degenerate primers were used successfully to characterize over 160 diverse aroA-like sequences from 10 geographically isolated, arsenic-contaminated sites and from 13 arsenite-oxidizing organisms. The primer sets were also useful for confirming the expression of aroA-like genes in an arsenite-oxidizing organism and in geothermal environments where arsenite is oxidized to arsenate. The phylogenetic and ecological diversity of aroA-like sequences obtained from this study suggests that genes for aerobic arsenite oxidation are widely distributed in the bacterial domain, are widespread in soil-water systems containing As, and play a critical role in the biogeochemical cycling of As.