Genome streamlining in a cosmopolitan oceanic bacterium

Novel Insights Into Bacterial Dimethylsulfoniopropionate Catabolism in the East China Sea

The compatible solute dimethylsulfoniopropionate (DMSP), made by many marine organisms, is one of Earth's most abundant organosulfur molecules. Many marine bacteria import DMSP and can degrade it as a source of carbon and/or sulfur via DMSP cleavage or DMSP demethylation pathways, which can generate the climate active gases dimethyl sulfide (DMS) or methanthiol (MeSH), respectively. Here we used culture-dependent and -independent methods to study bacteria catabolizing DMSP in the East China Sea (ECS). Of bacterial isolates, 42.11% showed DMSP-dependent DMS (Ddd⁺) activity, and 12.28% produced detectable levels of MeSH. Interestingly, although most Ddd⁺ isolates were Alphaproteobacteria (mainly Roseobacters), many gram-positive Actinobacteria were also shown to cleave DMSP producing DMS. The mechanism by which these Actinobacteria cleave DMSP is unknown, since no known functional ddd genes have been identified in genome sequences of Ddd⁺Microbacterium and Agrococcus isolates or in any other sequenced Actinobacteria genomes. Gene probes to the DMSP demethylation gene dmdA and the DMSP lyase gene dddP demonstrated that these DMSP-degrading genes are abundant and widely distributed in ECS seawaters. dmdA was present in relatively high proportions in both surface (19.53% ± 6.70%) and bottom seawater bacteria (16.00% ± 8.73%). In contrast, dddP abundance positively correlated with chlorophyll a, and gradually decreased with the distance from land, which implies that the bacterial DMSP lyase gene dddP might be from bacterial groups that closely associate with phytoplankton. Bacterial community analysis showed positive correlations between Rhodobacteraceae abundance and concentrations of DMS and DMSP, further confirming the link between this abundant bacterial class and the environmental DMSP cycling.

Occurrence and Fate of Ultramicrobacteria in a Full-Scale Drinking Water Treatment Plant

Ultramicrobacteria (UMB) are omnipresent and numerically dominate in freshwater, as microbes can present in drinking water systems, however, the UMB communities that occur and their removal behaviors remain poorly characterized in drinking water treatment plants (DWTPs). To gain insights into these issues, we profiled bacterial cell density, community structure and functions of UMB and their counterpart large bacteria (LB) using flow cytometry and filtration paired with 16S rRNA gene high-throughput sequencing in a full-scale DWTP. Contrary to the reduction of bacterial density and diversity, the proportion of UMB in the total bacteria community increased as the drinking water treatment process progressed, and biological activated carbon facilitated bacterial growth. Moreover, UMB were less diverse than LB, and their community structure and predicted functions were significantly different. In the DWTP, UMB indicator taxa were mainly affiliated with α/β/γ-Proteobacteria, Deinococcus-Thermus, Firmicutes, Acidobacteria, and Dependentiae. In particular, the exclusive clustering of UMB at the phylum level, e.g., Parcubacteria, Elusimicrobia, and Saccharibacteria, confirmed the fact that the ultra-small size of UMB is a naturally and evolutionarily conserved trait. Additionally, the streamlined genome could be connected to UMB, such as candidate phyla radiation (CPR) bacteria, following a symbiotic or parasitic lifestyle, which then leads to the observed high connectedness, i.e., non-random intra-taxa co-occurrence patterns within UMB. Functional prediction analysis revealed that environmental information processing and DNA replication and repair likely contribute to the higher resistance of UMB to drinking water treatment processes in comparison to LB. Overall, the study provides valuable insights into the occurrence and fate of UMB regarding community structure, phylogenetic characteristics and potential functions in a full-scale DWTP, and it is a useful reference for beneficial manipulation of the drinking water microbiome.

Characterization of bacterioplankton communities and quantification of organic carbon pools off the Galapagos Archipelago under contrasting environmental conditions

Bacteria play a crucial role in the marine carbon cycle, contributing to the production and degradation of organic carbon. Here, we investigated organic carbon pools, aggregate formation, and bacterioplankton communities in three contrasting oceanographic settings in the Galapagos Archipelago. We studied a submarine CO₂ vent at Roca Redonda (RoR), an upwelling site at Bolivar Channel (BoC) subjected to a weak El Niño event at the time of sampling in October 2014, as well as a site without volcanic or upwelling influence at Cowley Islet (CoI). We recorded physico-chemical parameters, and quantified particulate and dissolved organic carbon, transparent exopolymeric particles, and the potential of the water to form larger marine aggregates. Free-living and particle-attached bacterial communities were assessed via 16S rRNA gene sequencing. Both RoR and BoC exhibited temperatures elevated by 1–1.5 °C compared to CoI. RoR further experienced reduced pH between 6.8 and 7.4. We observed pronounced differences in organic carbon pools at each of the three sites, with highest dissolved organic carbon concentrations at BoC and RoR, and highest particulate organic carbon concentrations and aggregate formation at BoC. Bacterioplankton communities at BoC were dominated by opportunistic copiotrophic taxa, such as Alteromonas and Roseobacter, known to thrive in phytoplankton blooms, as opposed to oligotrophic taxa dominating at CoI, such as members of the SAR11 clade. Therefore, we propose that bacterial communities were mainly influenced by the availability of organic carbon at the investigated sites. Our study provides a comprehensive characterization of organic carbon pools and bacterioplankton communities, highlighting the high heterogeneity of various components of the marine carbon cycle around the Galapagos Archipelago.

A CAZyme-Rich Genome of a Taxonomically Novel Rhodophyte-Associated Carrageenolytic Marine Bacterium

Carbohydrate-active enzymes (CAZymes) have significant biotechnological potential as agents for degradation or modification of polysaccharides/glycans. As marine macroalgae are known to be rich in various types of polysaccharides, seaweed-associated bacteria are likely to be a good source of these CAZymes. A genomics approach can be used to explore CAZyme abundance and diversity, but it can also provide deep insights into the biology of CAZyme producers and, in particular, into molecular mechanisms that mediate their interaction with their hosts. In this study, a Gram-negative, aerobic, rod-shaped, carrageenolytic, and culturable marine bacterium designated as AOL6 was isolated from a diseased thallus of a carrageenan-producing farmed rhodophyte, Kappaphycus alvarezii (Gigartinales, Rhodophyta). The whole genome of this bacterium was sequenced and characterized. Sequence reads were assembled producing a high-quality genome assembly. The estimated genome size of the bacterium is 4.4 Mb and a G+C content of 52%. Molecular phylogenetic analysis based on a complete sequence of 16S rRNA, rpoB, and a set of 38 single-copy genes suggests that the bacterium is an unknown species and represents a novel genus in the family Cellvibrionaceae that is most closely related to the genera Teredinibacter and Saccharophagus. Genome comparison with T. turnerae T7901 and S. degradans 2-40 reveals several features shared by the three species, including a large number of CAZymes that comprised > 5% of the total number of protein-coding genes. The high proportion of CAZymes found in the AOL6 genome exceeds that of other known carbohydrate degraders, suggesting a significant capacity to degrade a range of polysaccharides including κ-carrageenan; 34% of these CAZymes have signal peptide sequences for secretion. Three putative κ-carrageenase-encoding genes were identified from the genome of the bacterium via in silico analysis, consistent with the results of the zymography assay (with κ-carrageenan as substrate). Genome analysis also indicated that AOL6 relies exclusively on type 2 secretion system (T2SS) for secreting proteins (possibly including glycoside hydrolases). In relation to T2SS, the product of the pilZ gene was predicted to be highly expressed, suggesting specialization for cell adhesion and secretion of virulence factors. The assignment of proteins to clusters of orthologous groups (COGs) revealed a pattern characteristic of r-strategists. Majority of two-component system proteins identified in the AOL6 genome were also predicted to be involved in chemotaxis and surface colonization. These genomic features suggest that AOL6 is an opportunistic pathogen, adapted to colonizing polysaccharide-rich hosts, including carrageenophytes.

Ecological selection for small microbial genomes along a temperate-to-thermal soil gradient

Small bacterial and archaeal genomes provide insights into the minimal requirements for life¹ and are phylogenetically widespread². However, the precise environmental pressures that constrain genome size in free-living microorganisms are unknown. A study including isolates has shown that thermophiles and other bacteria with high optimum growth temperatures often have small genomes³. It is unclear whether this relationship extends generally to microorganisms in nature^4,5 and more specifically to microorganisms that inhabit complex and highly variable environments, such as soils^3,6,7. To understand the genomic traits of thermally adapted microorganisms, here we investigated metagenomes from a 45 °C gradient of temperate-to-thermal soils that lie over the ongoing Centralia, Pennsylvania (USA) coal-seam fire. We found that hot soils harboured distinct communities with small genomes and small cell sizes relative to those in ambient soils. Hot soils notably lacked genes that encode known two-component regulatory systems, and antimicrobial production and resistance genes. Our results provide field evidence for the inverse relationship between microbial genome size and temperature in a diverse, free-living community over a wide range of temperatures that support microbial life.

Proteorhodopsins dominate the expression of phototrophic mechanisms in seasonal and dynamic marine picoplankton communities

The most abundant and ubiquitous microbes in the surface ocean use light as an energy source, capturing it via complex chlorophyll-based photosystems or simple retinal-based rhodopsins. Studies in various ocean regimes compared the abundance of these mechanisms, but few investigated their expression. Here we present the first full seasonal study of abundance and expression of light-harvesting mechanisms (proteorhodopsin, PR; aerobic anoxygenic photosynthesis, AAnP; and oxygenic photosynthesis, PSI) from deep-sequenced metagenomes and metatranscriptomes of marine picoplankton (<1 µm) at three coastal stations of the San Pedro Channel in the Pacific Ocean. We show that, regardless of season or sampling location, the most common phototrophic mechanism in metagenomes of this dynamic region was PR (present in 65–104% of the genomes as estimated by single-copy recA), followed by PSI (5–104%) and AAnP (5–32%). Furthermore, the normalized expression (RNA to DNA ratio) of PR genes was higher than that of oxygenic photosynthesis (average ± standard deviation 26.2 ± 8.4 vs. 11 ± 9.7), and the expression of the AAnP marker gene was significantly lower than both mechanisms (0.013 ± 0.02). We demonstrate that PR expression was dominated by the SAR11-cluster year-round, followed by other Alphaproteobacteria, unknown-environmental clusters and Gammaproteobacteria. This highly dynamic system further allowed us to identify a trend for PR spectral tuning, in which blue-absorbing PR genes dominate in areas with low chlorophyll-a concentrations (<0.25 µgL⁻¹). This suggests that PR phototrophy is not an accessory function but instead a central mechanism that can regulate photoheterotrophic population dynamics.

Large Diversity of Nonstandard Genes and Dynamic Evolution of Chloroplast Genomes in Siphonous Green Algae (Bryopsidales, Chlorophyta)

Chloroplast genomes have undergone tremendous alterations through the evolutionary history of the green algae (Chloroplastida). This study focuses on the evolution of chloroplast genomes in the siphonous green algae (order Bryopsidales). We present five new chloroplast genomes, which along with existing sequences, yield a data set representing all but one families of the order. Using comparative phylogenetic methods, we investigated the evolutionary dynamics of genomic features in the order. Our results show extensive variation in chloroplast genome architecture and intron content. Variation in genome size is accounted for by the amount of intergenic space and freestanding open reading frames that do not show significant homology to standard plastid genes. We show the diversity of these nonstandard genes based on their conserved protein domains, which are often associated with mobile functions (reverse transcriptase/intron maturase, integrases, phage- or plasmid-DNA primases, transposases, integrases, ligases). Investigation of the introns showed proliferation of group II introns in the early evolution of the order and their subsequent loss in the core Halimedineae, possibly through RT-mediated intron loss.

Parallel Evolution of Genome Streamlining and Cellular Bioenergetics across the Marine Radiation of a Bacterial Phylum

Understanding long-term patterns of microbial evolution is critical to advancing our knowledge of past and present role microbial life in driving global biogeochemical cycles. Historically, it has been challenging to study the evolution of environmental microbes due to difficulties in obtaining genome sequences from lineages that could not be cultivated, but recent advances in metagenomics and single-cell genomics have begun to obviate many of these hurdles. Here we present an evolutionary genomic analysis of the Marinimicrobia, a diverse bacterial group that is abundant in the global ocean. We demonstrate that distantly related Marinimicrobia species that reside in similar habitats have converged to assume similar genome architectures and cellular bioenergetics, suggesting that common factors shape the evolution of a broad array of marine lineages. These findings broaden our understanding of the evolutionary forces that have given rise to microbial life in the contemporary ocean.

Diverse bacterial and archaeal lineages drive biogeochemical cycles in the global ocean, but the evolutionary processes that have shaped their genomic properties and physiological capabilities remain obscure. Here we track the genome evolution of the globally abundant marine bacterial phylum Marinimicrobia across its diversification into modern marine environments and demonstrate that extant lineages are partitioned between epipelagic and mesopelagic habitats. Moreover, we show that these habitat preferences are associated with fundamental differences in genomic organization, cellular bioenergetics, and metabolic modalities. Multiple lineages present in epipelagic niches independently acquired genes necessary for phototrophy and environmental stress mitigation, and their genomes convergently evolved key features associated with genome streamlining. In contrast, lineages residing in mesopelagic waters independently acquired nitrate respiratory machinery and a variety of cytochromes, consistent with the use of alternative terminal electron acceptors in oxygen minimum zones (OMZs). Further, while epipelagic clades have retained an ancestral Na⁺-pumping respiratory complex, mesopelagic lineages have largely replaced this complex with canonical H⁺-pumping respiratory complex I, potentially due to the increased efficiency of the latter together with the presence of the more energy-limiting environments deep in the ocean’s interior. These parallel evolutionary trends indicate that key features of genomic streamlining and cellular bioenergetics have occurred repeatedly and congruently in disparate clades and underscore the importance of environmental conditions and nutrient dynamics in driving the evolution of diverse bacterioplankton lineages in similar ways throughout the global ocean.

Complete genome of streamlined marine actinobacterium Pontimonas salivibrio strain CL-TW6T adapted to coastal planktonic lifestyle

BACKGROUND

Pontimonas salivibrio strain CL-TW6T (=KCCM 90105 = JCM18206) was characterized as the type strain of a new genus within the Actinobacterial family Microbacteriaceae. It was isolated from a coastal marine environment in which members of Microbactericeae have not been previously characterized.

RESULTS

The genome of P. salivibrio CL-TW6T was a single chromosome of 1,760,810 bp. Genomes of this small size are typically found in bacteria growing slowly in oligotrophic zones and said to be streamlined. Phylogenetic analysis showed it to represent a lineage originating in the Microbacteriaceae radiation occurring before the snowball Earth glaciations, and to have a closer relationship with some streamlined bacteria known through metagenomic data. Several genomic characteristics typical of streamlined bacteria are found: %G + C is lower than non-streamlined members of the phylum; there are a minimal number of rRNA and tRNA genes, fewer paralogs in most gene families, and only two sigma factors; there is a noticeable absence of some nonessential metabolic pathways, including polyketide synthesis and catabolism of some amino acids. There was no indication of any phage genes or plasmids, however, a system of active insertion elements was present. P. salivibrio appears to be unusual in having polyrhamnose-based cell wall oligosaccharides instead of mycolic acid or teichoic acid-based oligosaccharides. Oddly, it conducts sulfate assimilation apparently for sulfating cell wall components, but not for synthesizing amino acids. One gene family it has more of, rather than fewer of, are toxin/antitoxin systems, which are thought to down-regulate growth during nutrient deprivation or other stressful conditions.

CONCLUSIONS

Because of the relatively small number of paralogs and its relationship to the heavily characterized Mycobacterium tuberculosis, we were able to heavily annotate the genome of P. salivibrio CL-TW6T. Its streamlined status and relationship to streamlined metagenomic constructs makes it an important reference genome for study of the streamlining concept. The final evolutionary trajectory of CL-TW6 T was to adapt to growth in a non-oligotrophic coastal zone. To understand that adaptive process, we give a thorough accounting of gene content, contrasting with both oligotrophic streamlined bacteria and large genome bacteria, and distinguishing between genes derived by vertical and horizontal descent.

Nano-Sized and Filterable Bacteria and Archaea: Biodiversity and Function

Nano-sized and filterable microorganisms are thought to represent the smallest living organisms on earth and are characterized by their small size (50-400 nm) and their ability to physically pass through <0.45 μm pore size filters. They appear to be ubiquitous in the biosphere and are present at high abundance across a diverse range of habitats including oceans, rivers, soils, and subterranean bedrock. Small-sized organisms are detected by culture-independent and culture-dependent approaches, with most remaining uncultured and uncharacterized at both metabolic and taxonomic levels. Consequently, their significance in ecological roles remain largely unknown. Successful isolation, however, has been achieved for some species (e.g., Nanoarchaeum equitans and "Candidatus Pelagibacter ubique"). In many instances, small-sized organisms exhibit a significant genome reduction and loss of essential metabolic pathways required for a free-living lifestyle, making their survival reliant on other microbial community members. In these cases, the nano-sized prokaryotes can only be co-cultured with their 'hosts.' This paper analyses the recent data on small-sized microorganisms in the context of their taxonomic diversity and potential functions in the environment.

Modeling of the GC content of the substituted bases in bacterial core genomes

Background

The purpose of the present study was to examine the GC content of substituted bases (sbGC) in the core genomes of 35 bacterial species. Each species, or core genome, constituted genomes from at least 10 strains. We also wanted to explore whether sbGC for each strain was associated with the corresponding species’ core genome GC content (cgGC). We present a simple mathematical model that estimates sbGC from cgGC. The model assumes only that the estimated sbGC is a function of cgGC proportional to fixed AT→GC (α) and GC → AT (β) mutation rates. Non-linear regression was used to estimate parameters α and β from the empirical data described above.

Results

We found that sbGC for each strain showed a non-linear association with the corresponding cgGC with a bias towards higher GC content for most core genomes (66.3% of the strains), assuming as a null-hypothesis that sbGC should be approximately equal to cgGC. The most GC rich core genomes (i.e. approximately %GC > 60), on the other hand, exhibited slightly less GC-biased sbGC than expected. The best fitted regression model indicates that GC → AT mutation rates β = (1.91 ± 0.13) p < 0.001 are approximately (1.91/0.79) = 2.42 times as high, on average, as AT→GC α = (− 0.79 ± 0.25) p < 0.001 mutation rates. Whether the observed sbGC GC-bias for all but the most GC-rich prokaryotic species is due to selection, compensating for the GC → AT mutation bias, and/or selective neutral processes is currently debated. Residual standard error was found to be σ = 0.076 indicating estimated errors of sbGC to be approximately within ±15.2% GC (95% confidence interval) for the strains of all species in the study.

Conclusion

Not only did our mathematical model give reasonable estimates of sbGC it also provides further support to previous observations that mutation rates in prokaryotes exhibit a universal GC → AT bias that appears to be remarkably consistent between taxa.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4984-3) contains supplementary material, which is available to authorized users.

The microbial contribution to reactive oxygen species dynamics in marine ecosystems

This review surveys the current state of knowledge of the concentrations, sources and sinks of reactive oxygen species (ROS) in the ocean. Both abiotic and biotic factors contribute to ROS dynamics in seawater, and ROS can feature prominently in marine microbe-microbe interactions. The sun plays a key role in the production of ROS in the ocean, and consequently ROS concentrations are typically maximal in the sun-exposed surface. However, microbes can also contribute significantly to extracellular ROS. Production of superoxide is widespread within the microbial community, and may benefit the producers as antimicrobial agents or perhaps more generally, as a means of nutrient scavenging. Decomposition of hydrogen peroxide is a community-wide activity, though some members may play less significant roles in this process. The more reactive forms of ROS, singlet oxygen and the hydroxyl radical, may be less important as microbial stressors, as they tend to react with the chemicals in seawater before they can contact the cells. However, exceptions may exist for microbes attached to singlet oxygen-generating sinking particulate matter. Extracellular ROS thus plays an important role in the ecology of marine microbes, the full extent to which we are only beginning to appreciate.

Relative stability of ploidy in a marine Synechococcus across various growth conditions

Marine picocyanobacteria of the genus Synechococcus are ubiquitous phototrophs in oceanic systems. Consistent with these organisms occupying vast tracts of the nutrient impoverished ocean, most marine Synechococcus so far studied are monoploid, i.e., contain a single chromosome copy. The exception is the oligoploid strain Synechococcus sp. WH7803, which on average possesses around 4 chromosome copies. Here, we set out to understand the role of resource availability (through nutrient deplete growth) and physical stressors (UV, exposure to low and high temperature) in regulating ploidy level in this strain. Using qPCR to assay ploidy status we demonstrate the relative stability of chromosome copy number in Synechococcus sp. WH7803. Such robustness in maintaining an oligoploid status even under nutrient and physical stress is indicative of a fundamental role, perhaps facilitating recombination of damaged DNA regions as a result of prolonged exposure to oxidative stress, or allowing added flexibility in gene expression via possessing multiple alleles.

Cross-protection from hydrogen peroxide by helper microbes: the impacts on the cyanobacterium Prochlorococcus and other beneficiaries in marine communities

Hydrogen peroxide (HOOH) is a reactive oxygen species, derived from molecular oxygen, that is capable of damaging microbial cells. Surprisingly, the HOOH defence systems of some aerobes in the oxygenated marine environments are critically depleted, relative to model aerobes. For instance, the gene encoding catalase is absent in the numerically dominant photosynthetic cyanobacterium, Prochlorococcus. Accordingly, Prochlorococcus is highly susceptible to HOOH when exposed as pure cultures. Pure cultures do not exist in the marine environment, however. Catalase-positive community members can remove HOOH from the seawater medium, thus lowering the threat to Prochlorococcus and any other member that likewise lacks their own catalase. This cross-protection may constitute a loosely defined symbiosis, whereby the catalase-positive helper cells may benefit through the acquisition of nutrients released by the beneficiaries such as Prochlorococcus. Other members of the community that may be helped by the catalase-positive cells may include some lineages of Synechococcus - the sister genus of Prochlorococcus - as well as some lineages of SAR11 and ammonia oxidizing archaea and bacteria. The co-occurrence of catalase-positive and -negative members suggests that cross-protection from HOOH-mediated oxidative stress may play an important role in the construction of the marine microbial community.

Fine metagenomic profile of the Mediterranean stratified and mixed water columns revealed by assembly and recruitment

BACKGROUND

The photic zone of aquatic habitats is subjected to strong physicochemical gradients. To analyze the fine-scale variations in the marine microbiome, we collected seven samples from a single offshore location in the Mediterranean at 15 m depth intervals during a period of strong stratification, as well as two more samples during the winter when the photic water column was mixed. We were able to recover 94 new metagenome-assembled genomes (MAGs) from these metagenomes and examine the distribution of key marine microbes within the photic zone using metagenomic recruitment.

RESULTS

Our results showed significant differences in the microbial composition of different layers within the stratified photic water column. The majority of microorganisms were confined to discreet horizontal layers of no more than 30 m (stenobathic). Only a few such as members of the SAR11 clade appeared at all depths (eurybathic). During the winter mixing period, only some groups of bloomers such as Pseudomonas were favored. Although most microbes appeared in both seasons, some groups like the SAR116 clade and some Bacteroidetes and Verrucomicrobia seemed to disappear during the mixing period. Furthermore, we found that some microbes previously considered seasonal (e.g., Archaea or Actinobacteria) were living in deeper layers within the photic zone during the stratification period. A strong depth-related specialization was detected, not only at the taxonomic level but also at the functional level, even within the different clades, for the manipulation and uptake of specific polysaccharides. Rhodopsin sequences (green or blue) also showed narrow depth distributions that correlated with the taxonomy of the microbe in which they were found but not with depth.

CONCLUSIONS

Although limited to a single location in the Mediterranean, this study has profound implications for our understanding of how marine microbial communities vary with depth within the photic zone when stratified. Our results highlight the importance of collecting samples at different depths in the water column when comparing seasonal variations and have important ramifications for global marine studies that most often take samples from only one single depth. Furthermore, our perspective and approaches (metagenomic assembly and recruitment) are broadly applicable to other metagenomic studies.

Diversity and community structure of marine microbes around the Benham Rise underwater plateau, northeastern Philippines

Microbes are central to the structuring and functioning of marine ecosystems. Given the remarkable diversity of the ocean microbiome, uncovering marine microbial taxa remains a fundamental challenge in microbial ecology. However, there has been little effort, thus far, to describe the diversity of marine microorganisms in the region of high marine biodiversity around the Philippines. Here, we present data on the taxonomic diversity of bacteria and archaea in Benham Rise, Philippines, Western Pacific Ocean, using 16S V4 rRNA gene sequencing. The major bacterial and archaeal phyla identified in the Benham Rise are Proteobacteria, Cyanobacteria, Actinobacteria, Bacteroidetes, Marinimicrobia, Thaumarchaeota and, Euryarchaeota. The upper mesopelagic layer exhibited greater microbial diversity and richness compared to surface waters. Vertical zonation of the microbial community is evident and may be attributed to physical stratification of the water column acting as a dispersal barrier. Canonical Correspondence Analysis (CCA) recapitulated previously known associations of taxa and physicochemical parameters in the environment, such as the association of oligotrophic clades with low nutrient surface water and deep water clades that have the capacity to oxidize ammonia or nitrite at the upper mesopelagic layer. These findings provide foundational information on the diversity of marine microbes in Philippine waters. Further studies are warranted to gain a more comprehensive picture of microbial diversity within the region.

Mosaic patterns of B-vitamin synthesis and utilization in a natural marine microbial community

Aquatic environments contain large communities of microorganisms whose synergistic interactions mediate the cycling of major and trace nutrients, including vitamins. B-vitamins are essential coenzymes that many organisms cannot synthesize. Thus, their exchange among de novo synthesizers and auxotrophs is expected to play an important role in the microbial consortia and explain some of the temporal and spatial changes observed in diversity. In this study, we analyzed metatranscriptomes of a natural marine microbial community, diel sampled quarterly over one year to try to identify the potential major B-vitamin synthesizers and consumers. Transcriptomic data showed that the best-represented taxa dominated the expression of synthesis genes for some B-vitamins but lacked transcripts for others. For instance, Rhodobacterales dominated the expression of vitamin-B₁₂ synthesis, but not of vitamin-B₇ , whose synthesis transcripts were mainly represented by Flavobacteria. In contrast, bacterial groups that constituted less than 4% of the community (e.g., Verrucomicrobia) accounted for most of the vitamin-B₁ synthesis transcripts. Furthermore, ambient vitamin-B₁ concentrations were higher in samples collected during the day, and were positively correlated with chlorophyll-a concentrations. Our analysis supports the hypothesis that the mosaic of metabolic interdependencies through B-vitamin synthesis and exchange are key processes that contribute to shaping microbial communities in nature.

Genome Reduction in Psychromonas Species within the Gut of an Amphipod from the Ocean's Deepest Point

Amphipods are the dominant scavenging metazoan species in the Mariana Trench, the deepest known point in Earth's oceans. Here the gut microbiota of the amphipod Hirondellea gigas collected from the Challenger and Sirena Deeps of the Mariana Trench were investigated. The 11 amphipod individuals included for analyses were dominated by Psychromonas, of which a nearly complete genome was successfully recovered (designated CDP1). Compared with previously reported free-living Psychromonas strains, CDP1 has a highly reduced genome. Genome alignment showed deletion of the trimethylamine N-oxide (TMAO) reducing gene cluster in CDP1, suggesting that the "piezolyte" function of TMAO is more important than its function in respiration, which may lead to TMAO accumulation. In terms of nutrient utilization, the bacterium retains its central carbohydrate metabolism but lacks most of the extended carbohydrate utilization pathways, suggesting the confinement of Psychromonas to the host gut and sequestration from more variable environmental conditions. Moreover, CDP1 contains a complete formate hydrogenlyase complex, which might be involved in energy production. The genomic analyses imply that CDP1 may have developed adaptive strategies for a lifestyle within the gut of the hadal amphipod H. gigas. IMPORTANCE As a unique but poorly investigated habitat within marine ecosystems, hadal trenches have received interest in recent years. This study explores the gut microbial composition and function in hadal amphipods, which are among the dominant carrion feeders in hadal habitats. Further analyses of a dominant strain revealed genomic features that may contribute to its adaptation to the amphipod gut environment. Our findings provide new insights into animal-associated bacteria in the hadal biosphere.

Seasonal changes in the abundance of bacterial genes related to dimethylsulfoniopropionate catabolism in seawater from Ofunato Bay revealed by metagenomic analysis

Ofunato Bay is located in the northeastern Pacific Ocean area of Japan, and it has the highest biodiversity of marine organisms in the world, primarily due to tidal influences from the cold Oyashio and warm Kuroshio Currents. Our previous results from performing shotgun metagenomics indicated that Candidatus Pelagibacter ubique and Planktomarina temperata were the dominant bacteria (Reza et al., 2018a, 2018b). These bacteria are reportedly able to catabolize dimethylsulfoniopropionate (DMSP) produced from phytoplankton into dimethyl sulfide (DMS) or methanethiol (MeSH). This study was focused on seasonal changes in the abundances of bacterial genes (dddP, dmdA) related to DMSP catabolism in the seawater of Ofunato Bay by BLAST+ analysis using shotgun metagenomic datasets. We found seasonal changes among the Candidatus Pelagibacter ubique strains, including those of the HTCC1062 type and the Red Sea type. A good correlation was observed between the chlorophyll a concentrations and the abundances of the catabolic genes, suggesting that the bacteria directly interact with phytoplankton in the marine material cycle system and play important roles in producing DMS and MeSH from DMSP as signaling molecules for the possible formation of the scent of the tidewater or as fish attractants.

Metagenomic Insights Into the Microbial Community and Nutrient Cycling in the Western Subarctic Pacific Ocean

The composition and metabolic functions of prokaryotic communities in the western subarctic Pacific (WSP), where strong mixing of waters from the Sea of Okhotsk and the East Kamchatka Current result in transfer to the Oyashio Current, were investigated using a shotgun metagenome sequencing approach. Functional metabolic genes related to nutrient cycling of nitrogen, sulfur, carbohydrates, iron and amino acids were differently distributed between the surface and deep waters of the WSP. Genes related to nitrogen metabolism were mainly found in deep waters, where Thaumarchaeaota, Sphingomonadales, and Pseudomonadales were closely associated and performing important roles in ammonia oxidation, assimilatory nitrate reduction, and dissimilatory nitrate reduction processes, respectively. In addition, orders affiliated to Spingobacteria and Alphaproteobacteria were crucial for sulfate reduction and abundant at 3000 m, whereas orders affiliated to Gammaproteobacteria, which harbored the most sulfate reduction genes, were abundant at 1000 m. Additionally, when compared with the East Kamchatka Current, the prokaryotes in the Oyashio Current were likely to consume more energy for synthesizing cellular components. Also, genes encoding iron transport and siderophore biosynthesis proteins were in low abundance, indicating that the iron was not a limiting factor in the Oyashio current. In contrast, in the East Kamchatka Current, prokaryotes were more likely to directly utilize the amino acids and absorb iron from the environment. Overall, our data indicated that the transformation from the East Kamchatka Current to the Oyashio Current reshapes not only the composition of microbial community, but also the function of the metabolic processes. These results extended our knowledge of the microbial composition and potential metabolism in the WSP.

Cultivation and genomics of the first freshwater SAR11 (LD12) isolate

Evolutionary transitions between fresh and salt water happen infrequently among bacterioplankton. Within the ubiquitous and highly abundant heterotrophic Alphaproteobacteria order Pelagibacterales (SAR11), most members live in marine habitats, but the LD12 subclade has evolved as a unique freshwater lineage. LD12 cells occur as some of the most dominant freshwater bacterioplankton, yet this group has remained elusive to cultivation, hampering a more thorough understanding of its biology. Here, we report the first successful isolation of an LD12 representative, strain LSUCC0530, using high-throughput dilution-to-extinction cultivation methods, and its complete genome sequence. Growth experiments corroborate ecological data suggesting active populations of LD12 in brackish water up to salinities of ~5. LSUCC0530 has the smallest closed genome thus far reported for a SAR11 strain (1.16 Mbp). The genome affirms many previous metabolic predictions from cultivation-independent analyses, like a complete Embden–Meyerhof–Parnas glycolysis pathway, but also provides novel insights, such as the first isocitrate dehydrogenase in LD12, a likely homologous recombination of malate synthase from outside of the SAR11 clade, and analogous substitutions of ion transporters with others that occur throughout the rest of the SAR11 clade. Growth data support metagenomic recruitment results suggesting temperature-based ecotype diversification within LD12. Key gene losses for osmolyte uptake provide a succinct hypothesis for the evolutionary transition of LD12 from salt to freshwater. For strain LSUCC0530, we propose the provisional nomenclature Candidatus fonsibacter ubiquis.

Ocean biogeochemistry modeled with emergent trait-based genomics

Marine ecosystem models have advanced to incorporate metabolic pathways discovered with genomic sequencing, but direct comparisons between models and "omics" data are lacking. We developed a model that directly simulates metagenomes and metatranscriptomes for comparison with observations. Model microbes were randomly assigned genes for specialized functions, and communities of 68 species were simulated in the Atlantic Ocean. Unfit organisms were replaced, and the model self-organized to develop community genomes and transcriptomes. Emergent communities from simulations that were initialized with different cohorts of randomly generated microbes all produced realistic vertical and horizontal ocean nutrient, genome, and transcriptome gradients. Thus, the library of gene functions available to the community, rather than the distribution of functions among specific organisms, drove community assembly and biogeochemical gradients in the model ocean.

Proteorhodopsin variability and distribution in the North Pacific Subtropical Gyre

Proteorhodopsin is a light-activated retinal-containing proton pump found in many marine bacteria. These photoproteins are globally distributed in the ocean’s photic zone and are capable of generating a proton motive force across the cell membrane. We investigated the phylogenetic diversity, distribution, and abundance of proteorhodopsin encoding genes in free-living bacterioplankton in the North Pacific Subtropical Gyre, leveraging a gene catalog derived from metagenomic samples from the ocean’s surface to 1000 m depth. Proteorhodopsin genes were identified at all depths sampled, but were most abundant at depths shallower than 200 m. The majority of proteorhodopsin gene sequences (60.9%) belonged to members of the SAR11 lineage, with remaining sequences distributed among other diverse taxa. We observed variations in the conserved residues involved in ion pumping and spectral tuning, and biochemically confirmed four different proton pumping proteorhodopsin motifs, including one unique to deep-water SAR11. We also identified a new group of putative proteorhodopsins having unknown function. Our results reveal a broad organismal and unexpected depth distribution for different proteorhodopsin types, as well as substantial within-taxon variability. These data provide a framework for exploring the ecological relevance of proteorhodopsins and their spatiotemporal variation and function in heterotrophic bacteria in the open ocean.

Competitive resource allocation to metabolic pathways contributes to overflow metabolisms and emergent properties in cross-feeding microbial consortia

Resource scarcity is a common stress in nature and has a major impact on microbial physiology. This review highlights microbial acclimations to resource scarcity, focusing on resource investment strategies for chemoheterotrophs from the molecular level to the pathway level. Competitive resource allocation strategies often lead to a phenotype known as overflow metabolism; the resulting overflow byproducts can stabilize cooperative interactions in microbial communities and can lead to cross-feeding consortia. These consortia can exhibit emergent properties such as enhanced resource usage and biomass productivity. The literature distilled here draws parallels between in silico and laboratory studies and ties them together with ecological theories to better understand microbial stress responses and mutualistic consortia functioning.

Functional Genomics and Phylogenetic Evidence Suggest Genus-Wide Cobalamin Production by the Globally Distributed Marine Nitrogen Fixer Trichodesmium

Only select prokaryotes can biosynthesize vitamin B₁₂ (i.e., cobalamins), but these organic co-enzymes are required by all microbial life and can be vanishingly scarce across extensive ocean biomes. Although global ocean genome data suggest cyanobacteria to be a major euphotic source of cobalamins, recent studies have highlighted that >95% of cyanobacteria can only produce a cobalamin analog, pseudo-B₁₂, due to the absence of the BluB protein that synthesizes the α ligand 5,6-dimethylbenzimidizole (DMB) required to biosynthesize cobalamins. Pseudo-B₁₂ is substantially less bioavailable to eukaryotic algae, as only certain taxa can intracellularly remodel it to one of the cobalamins. Here we present phylogenetic, metagenomic, transcriptomic, proteomic, and chemical analyses providing multiple lines of evidence that the nitrogen-fixing cyanobacterium Trichodesmium transcribes and translates the biosynthetic, cobalamin-requiring BluB enzyme. Phylogenetic evidence suggests that the Trichodesmium DMB biosynthesis gene, bluB, is of ancient origin, which could have aided in its ecological differentiation from other nitrogen-fixing cyanobacteria. Additionally, orthologue analyses reveal two genes encoding iron-dependent B₁₂ biosynthetic enzymes (cbiX and isiB), suggesting that iron availability may be linked not only to new nitrogen supplies from nitrogen fixation, but also to B₁₂ inputs by Trichodesmium. These analyses suggest that Trichodesmium contains the genus-wide genomic potential for a previously unrecognized role as a source of cobalamins, which may prove to considerably impact marine biogeochemical cycles.

Comparative genomic analysis reveals the evolution and environmental adaptation strategies of vibrios

BACKGROUND

Vibrios are among the most diverse and ecologically important marine bacteria, which have evolved many characteristics and lifestyles to occupy various niches. The relationship between genome features and environmental adaptation strategies is an essential part for understanding the ecological functions of vibrios in the marine system. The advent of complete genome sequencing technology has provided an important method of examining the genetic characteristics of vibrios on the genomic level.

RESULTS

Two Vibrio genomes were sequenced and found to occupy many unique orthologues families which absent from the previously genes pool of the complete genomes of vibrios. Comparative genomics analysis found vibrios encompass a steady core-genome and tremendous pan-genome with substantial gene gain and horizontal gene transfer events in the evolutionary history. Evolutionary analysis based on the core-genome tree suggested that V. fischeri emerged ~ 385 million years ago, along with the occurrence of cephalopods and the flourish of fish. The relatively large genomes, the high number of 16S rRNA gene copies, and the presence of R-M systems and CRISPR system help vibrios live in various marine environments. Chitin-degrading related genes are carried in nearly all the Vibrio genomes. The number of chitinase genes in vibrios has been extremely expanded compared to which in the most recent ancestor of the genus. The chitinase A genes were estimated to have evolved along with the genus, and have undergone significant purifying selective force to conserve the ancestral state.

CONCLUSIONS

Vibrios have experienced extremely genome expansion events during their evolutionary history, allowing them to develop various functions to spread globally. Despite their close phylogenetic relationships, vibrios were found to have a tremendous pan-genome with a steady core-genome, which indicates the highly plastic genome of the genus. Additionally, the existence of various chitin-degrading related genes and the expansion of chitinase A in the genus demonstrate the importance of the chitin utilization for vibrios. Defensive systems in the Vibrio genomes may protect them from the invasion of external DNA. These genomic features investigated here provide a better knowledge of how the evolutionary process has forged Vibrio genomes to occupy various niches.

The impact of depuration on mussel hepatopancreas bacteriome composition and predicted metagenome

Due to the rapid elimination of bacteria through normal behaviour of filter feeding and excretion, the decontamination of hazardous contaminating bacteria from shellfish is performed by depuration. This process, under conditions that maximize shellfish filtering activity, is a useful method to eliminate microorganisms from bivalves. The microbiota composition in bivalves reflects that of the environment of harvesting waters, so quite different bacteriomes would be expected in shellfish collected in different locations. Bacterial accumulation within molluscan shellfish occurs primarily in the hepatopancreas. In order to assess the effect of the depuration process on these different bacteriomes, in this work we used 16S RNA pyrosequencing and metagenome prediction to assess the impact of 15 h of depuration on the whole hepatopancreas bacteriome of mussels collected in three different locations.

Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics

For many bacteria with sequenced genomes, we do not understand how they synthesize some amino acids. This makes it challenging to reconstruct their metabolism, and has led to speculation that bacteria might be cross-feeding amino acids. We studied heterotrophic bacteria from 10 different genera that grow without added amino acids even though an automated tool predicts that the bacteria have gaps in their amino acid synthesis pathways. Across these bacteria, there were 11 gaps in their amino acid biosynthesis pathways that we could not fill using current knowledge. Using genome-wide mutant fitness data, we identified novel enzymes that fill 9 of the 11 gaps and hence explain the biosynthesis of methionine, threonine, serine, or histidine by bacteria from six genera. We also found that the sulfate-reducing bacterium Desulfovibrio vulgaris synthesizes homocysteine (which is a precursor to methionine) by using DUF39, NIL/ferredoxin, and COG2122 proteins, and that homoserine is not an intermediate in this pathway. Our results suggest that most free-living bacteria can likely make all 20 amino acids and illustrate how high-throughput genetics can uncover previously-unknown amino acid biosynthesis genes.

For a few bacteria, it is well known how they can make all 20 of the standard amino acids (the building blocks of proteins). For many other bacteria, their genome sequence implies that there are gaps in these biosynthetic pathways, so that the bacteria cannot make all of the amino acids and would need to take up some of them from their environment instead. But many bacteria can grow in minimal media (without any amino acids) despite these apparent gaps. We studied 10 bacteria with predicted gaps in amino acid biosynthesis that nevertheless grow in minimal media. Most of these gaps were spurious, but 11 of the gaps were genuine and could not be explained by current knowledge. Using high-throughput genetics, we systematically identified genes that were required for growth in minimal media and identified the biosynthetic genes that fill 9 of the 11 gaps. We hope that this approach can be applied to many more bacteria and will eventually allow us to accurately predict the nutritional requirements of a bacterium from its genome sequence.

Genomes of Novel Microbial Lineages Assembled from the Sub-Ice Waters of Lake Baikal

We present a metagenomic study of Lake Baikal (East Siberia). Two samples obtained from the water column under the ice cover (5 and 20 m deep) in March 2016 have been deep sequenced and the reads assembled to generate metagenome-assembled genomes (MAGs) that are representative of the microbes living in this special environment. Compared with freshwater bodies studied around the world, Lake Baikal had an unusually high fraction of Verrucomicrobia Other groups, such as Actinobacteria and Proteobacteria, were in proportions similar to those found in other lakes. The genomes (and probably cells) tended to be small, presumably reflecting the extremely oligotrophic and cold prevalent conditions. Baikal microbes are novel lineages recruiting very little from other water bodies and are distantly related to other freshwater microbes. Despite their novelty, they showed the closest relationship to genomes discovered by similar approaches from other freshwater lakes and reservoirs. Some of them were particularly similar to MAGs from the Baltic Sea, which, although it is brackish, connected to the ocean, and much more eutrophic, has similar climatological conditions. Many of the microbes contained rhodopsin genes, indicating that, in spite of the decreased light penetration allowed by the thick ice/snow cover, photoheterotrophy could be widespread in the water column, either because enough light penetrates or because the microbes are already adapted to the summer ice-less conditions. We have found a freshwater SAR11 subtype I/II representative showing striking synteny with Pelagibacterubique strains, as well as a phage infecting the widespread freshwater bacterium PolynucleobacterIMPORTANCE Despite the increasing number of metagenomic studies on different freshwater bodies, there is still a missing component in oligotrophic cold lakes suffering from long seasonal frozen cycles. Here, we describe microbial genomes from metagenomic assemblies that appear in the upper water column of Lake Baikal, the largest and deepest freshwater body on Earth. This lake is frozen from January to May, which generates conditions that include an inverted temperature gradient (colder up), decrease in light penetration due to ice, and, especially, snow cover, and oligotrophic conditions more similar to the open-ocean and high-altitude lakes than to other freshwater or brackish systems. As could be expected, most reconstructed genomes are novel lineages distantly related to others in cold environments, like the Baltic Sea and other freshwater lakes. Among them, there was a broad set of streamlined microbes with small genomes/intergenic spacers, including a new nonmarine Pelagibacter-like (subtype I/II) genome.

Rokubacteria: Genomic Giants among the Uncultured Bacterial Phyla

Recent advances in single-cell genomic and metagenomic techniques have facilitated the discovery of numerous previously unknown, deep branches of the tree of life that lack cultured representatives. Many of these candidate phyla are composed of microorganisms with minimalistic, streamlined genomes lacking some core metabolic pathways, which may contribute to their resistance to growth in pure culture. Here we analyzed single-cell genomes and metagenome bins to show that the "Candidate phylum Rokubacteria," formerly known as SPAM, represents an interesting exception, by having large genomes (6-8 Mbps), high GC content (66-71%), and the potential for a versatile, mixotrophic metabolism. We also observed an unusually high genomic heterogeneity among individual Rokubacteria cells in the studied samples. These features may have contributed to the limited recovery of sequences of this candidate phylum in prior cultivation and metagenomic studies. Our analyses suggest that Rokubacteria are distributed globally in diverse terrestrial ecosystems, including soils, the rhizosphere, volcanic mud, oil wells, aquifers, and the deep subsurface, with no reports from marine environments to date.

Bacterial Succession on Sinking Particles in the Ocean's Interior

Sinking particles formed in the photic zone and moving vertically through the water column are a main mechanism for nutrient transport to the deep ocean, and a key component of the biological carbon pump. The particles appear to be processed by a microbial community substantially different from the surrounding waters. Single cell genomics and metagenomics were employed to describe the succession of dominant bacterial groups during particle processing. Sinking particles were extracted from sediment traps at Station Aloha in the North Pacific Subtropical Gyre (NPSG) during two different trap deployments conducted in July and August 2012. The microbial communities in poisoned vs. live sediment traps differed significantly from one another, consistent with prior observations by Fontanez et al. (2015). Partial genomes from these communities were sequenced from cells belonging to the genus Arcobacter (commensalists potentially associated with protists such as Radiolaria), and Vibrio campbellii (a group previously reported to be associated with crustacea). These bacteria were found in the particle-associated communities at specific depths in both trap deployments, presumably due to their specific host-associations. Partial genomes were also sequenced from cells belonging to Idiomarina and Kangiella that were enriched in live traps over a broad depth range, that represented a motile copiotroph and a putatively non-motile algicidal saprophyte, respectively. Planktonic bacterial cells most likely caught in the wake of the particles belonging to Actinomarina and the SAR11 clade were also sequenced. Our results suggest that similar groups of eukaryote-associated bacteria are consistently found on sinking particles at different times, and that particle remineralization involves specific, reproducible bacterial succession events in oligotrophic ocean waters.

Why Might Bacterial Pathogens Have Small Genomes?

Bacteria that cause serious disease often have smaller genomes, and fewer genes, than their nonpathogenic, or less pathogenic relatives. Here, we review evidence for the generality of this association, and summarise the various reasons why the association might hold. We focus on the population genetic processes that might lead to reductive genome evolution, and show how several of these could be connected to pathogenicity. We find some evidence for most of the processes having acted in bacterial pathogens, including several different modes of genome reduction acting in the same lineage. We argue that predictable processes of genome evolution might not reflect any common underlying process.

Genome sequences of lower Great Lakes Microcystis sp. reveal strain-specific genes that are present and expressed in western Lake Erie blooms

Blooms of the potentially toxic cyanobacterium Microcystis are increasing worldwide. In the Laurentian Great Lakes they pose major socioeconomic, ecological, and human health threats, particularly in western Lake Erie. However, the interpretation of "omics" data is constrained by the highly variable genome of Microcystis and the small number of reference genome sequences from strains isolated from the Great Lakes. To address this, we sequenced two Microcystis isolates from Lake Erie (Microcystis aeruginosa LE3 and M. wesenbergii LE013-01) and one from upstream Lake St. Clair (M. cf aeruginosa LSC13-02), and compared these data to the genomes of seventeen Microcystis spp. from across the globe as well as one metagenome and seven metatranscriptomes from a 2014 Lake Erie Microcystis bloom. For the publically available strains analyzed, the core genome is ~1900 genes, representing ~11% of total genes in the pan-genome and ~45% of each strain's genome. The flexible genome content was related to Microcystis subclades defined by phylogenetic analysis of both housekeeping genes and total core genes. To our knowledge this is the first evidence that the flexible genome is linked to the core genome of the Microcystis species complex. The majority of strain-specific genes were present and expressed in bloom communities in Lake Erie. Roughly 8% of these genes from the lower Great Lakes are involved in genome plasticity (rapid gain, loss, or rearrangement of genes) and resistance to foreign genetic elements (such as CRISPR-Cas systems). Intriguingly, strain-specific genes from Microcystis cultured from around the world were also present and expressed in the Lake Erie blooms, suggesting that the Microcystis pangenome is truly global. The presence and expression of flexible genes, including strain-specific genes, suggests that strain-level genomic diversity may be important in maintaining Microcystis abundance during bloom events.

Effect of the environment on horizontal gene transfer between bacteria and archaea

Background

Horizontal gene transfer, the transfer and incorporation of genetic material between different species of organisms, has an important but poorly quantified role in the adaptation of microbes to their environment. Previous work has shown that genome size and the number of horizontally transferred genes are strongly correlated. Here we consider how genome size confuses the quantification of horizontal gene transfer because the number of genes an organism accumulates over time depends on its evolutionary history and ecological context (e.g., the nutrient regime for which it is adapted).

Results

We investigated horizontal gene transfer between archaea and bacteria by first counting reciprocal BLAST hits among 448 bacterial and 57 archaeal genomes to find shared genes. Then we used the DarkHorse algorithm, a probability-based, lineage-weighted method (Podell & Gaasterland, 2007), to identify potential horizontally transferred genes among these shared genes. By removing the effect of genome size in the bacteria, we have identified bacteria with unusually large numbers of shared genes with archaea for their genome size. Interestingly, archaea and bacteria that live in anaerobic and/or high temperature conditions are more likely to share unusually large numbers of genes. However, high salt was not found to significantly affect the numbers of shared genes. Numbers of shared (genome size-corrected, reciprocal BLAST hits) and transferred genes (identified by DarkHorse) were strongly correlated. Thus archaea and bacteria that live in anaerobic and/or high temperature conditions are more likely to share horizontally transferred genes. These horizontally transferred genes are over-represented by genes involved in energy conversion as well as the transport and metabolism of inorganic ions and amino acids.

Conclusions

Anaerobic and thermophilic bacteria share unusually large numbers of genes with archaea. This is mainly due to horizontal gene transfer of genes from the archaea to the bacteria. In general, these transfers are from archaea that live in similar oxygen and temperature conditions as the bacteria that receive the genes. Potential hotspots of horizontal gene transfer between archaea and bacteria include hot springs, marine sediments, and oil wells. Cold spots for horizontal transfer included dilute, aerobic, mesophilic environments such as marine and freshwater surface waters.

Drivers of interannual variability in virioplankton abundance at the coastal western Antarctic peninsula and the potential effects of climate change

An 8-year time-series in the Western Antarctic Peninsula (WAP) with an approximately weekly sampling frequency was used to elucidate changes in virioplankton abundance and their drivers in this climatically sensitive region. Virioplankton abundances at the coastal WAP show a pronounced seasonal cycle with interannual variability in the timing and magnitude of the summer maxima. Bacterioplankton abundance is the most influential driving factor of the virioplankton, and exhibit closely coupled dynamics. Sea ice cover and duration predetermine levels of phytoplankton stock and thus, influence virioplankton by dictating the substrates available to the bacterioplankton. However, variations in the composition of the phytoplankton community and particularly the prominence of Diatoms inferred from silicate drawdown, drive interannual differences in the magnitude of the virioplankton bloom; likely again mediated through changes in the bacterioplankton. Their findings suggest that future warming within the WAP will cause changes in sea ice that will influence viruses and their microbial hosts through changes in the timing, magnitude and composition of the phytoplankton bloom. Thus, the flow of matter and energy through the viral shunt may be decreased with consequences for the Antarctic food web and element cycling.

Taxonomic and chemical assessment of exceptionally abundant rock mine biofilm

BACKGROUND

An exceptionally thick biofilm covers walls of ancient gold and arsenic Złoty Stok mine (Poland) in the apparent absence of organic sources of energy.

METHODS AND RESULTS

We have characterized this microbial community using culture-dependent and independent methods. We sequenced amplicons of the 16S rRNA gene obtained using generic primers and additional primers targeted at Archaea and Actinobacteria separately. Also, we have cultured numerous isolates from the biofilm on different media under aerobic and anaerobic conditions. We discovered very high biodiversity, and no single taxonomic group was dominant. The majority of almost 4,000 OTUs were classified above genus level indicating presence of novel species. Elemental analysis, performed using SEM-EDS and X-ray, of biofilm samples showed that carbon, sulphur and oxygen were not evenly distributed in the biofilm and that their presence is highly correlated. However, the distribution of arsenic and iron was more flat, and numerous intrusions of elemental silver and platinum were noted, indicating that microorganisms play a key role in releasing these elements from the rock.

CONCLUSIONS

Altogether, the picture obtained throughout this study shows a very rich, complex and interdependent system of rock biofilm. The chemical heterogeneity of biofilm is a likely explanation as to why this oligotrophic environment is capable of supporting such high microbial diversity.

Environmental drivers of a microbial genomic transition zone in the ocean's interior

The core properties of microbial genomes, including GC content and genome size, are known to vary widely among different bacteria and archaea ^1,2 . Several hypotheses have been proposed to explain this genomic variability, but the fundamental drivers that shape bacterial and archaeal genomic properties remain uncertain ^3-7 . Here, we report the existence of a sharp genomic transition zone below the photic zone, where bacterial and archaeal genomes and proteomes undergo a community-wide punctuated shift. Across a narrow range of increasing depth of just tens of metres, diverse microbial clades trend towards larger genome size, higher genomic GC content, and proteins with higher nitrogen but lower carbon content. These community-wide changes in genome features appear to be driven by gradients in the surrounding environmental energy and nutrient fields. Collectively, our data support hypotheses invoking nutrient limitation as a central driver in the evolution of core bacterial and archaeal genomic and proteomic properties.

Microbial communities in the reef water at Kham Island, lower Gulf of Thailand

Coral reefs are among the most biodiverse habitats on Earth, but knowledge of their associated marinemicrobiome remains limited. To increase the understanding of the coral reef ecosystem in the lower Gulf of Thailand, this study utilized 16S and 18S rRNA gene-based pyrosequencing to identify the prokaryotic and eukaryotic microbiota present in the reef water at Kham Island, Trat province, Thailand (N6.97 E100.86). The obtained result was then compared with the published microbiota from different coral reef water and marine sites. The coral reefs at Kham Island are of the fringe type. The reefs remain preserved and abundant. The community similarity indices (i.e., Lennon similarity index, Yue & Clayton similarity index) indicated that the prokaryotic composition of Kham was closely related to that of Kra, another fringing reef site in the lower Gulf of Thailand, followed by coral reef water microbiota at GS048b (Cooks Bay, Fr. Polynesia), Palmyra (Northern Line Islands, United States) and GS108b (Coccos Keeling, Australia), respectively. Additionally, the microbial eukaryotic populations at Kham was analyzed and compared with the available database at Kra. Both eukaryotic microbiota, in summer and winter seasons, were correlated. An abundance of Dinophysis acuminata was noted in the summer season, in accordance with its reported cause of diarrhoeatic shellfish outbreak in the summer season elsewhere. The slightly lower biodiversity in Kham than at Kra might reflect the partly habitat difference due to coastal anthropogenic activities and minor water circulation, as Kham locates close to the mainland and is surrounded by islands (e.g., Chang and Kut islands). The global marine microbiota comparison suggested relatively similar microbial structures among coral sites irrespective of geographical location, supporting the importance of coral-associated marine microbiomes, and Spearman’s correlation analysis between community membership and factors of shore distance and seawater temperature indicated potential correlation of these factors (p-values < 0.05) with Kham, Kra, and some other coral and coastal sites. Together, this study provided the second marine microbial database for the coral reef of the lower Gulf of Thailand, and a comparison of the coral-associated marine microbial diversity among global ocean sites.

Investigating the Biosynthesis of Natural Products from Marine Proteobacteria: A Survey of Molecules and Strategies

The phylum proteobacteria contains a wide array of Gram-negative marine bacteria. With recent advances in genomic sequencing, genome analysis, and analytical chemistry techniques, a whole host of information is being revealed about the primary and secondary metabolism of marine proteobacteria. This has led to the discovery of a growing number of medically relevant natural products, including novel leads for the treatment of multidrug-resistant Staphylococcus aureus (MRSA) and cancer. Of equal interest, marine proteobacteria produce natural products whose structure and biosynthetic mechanisms differ from those of their terrestrial and actinobacterial counterparts. Notable features of secondary metabolites produced by marine proteobacteria include halogenation, sulfur-containing heterocycles, non-ribosomal peptides, and polyketides with unusual biosynthetic logic. As advances are made in the technology associated with functional genomics, such as computational sequence analysis, targeted DNA manipulation, and heterologous expression, it has become easier to probe the mechanisms for natural product biosynthesis. This review will focus on genomics driven approaches to understanding the biosynthetic mechanisms for natural products produced by marine proteobacteria.

Phage-host associations in a full-scale activated sludge plant during sludge bulking

Sludge bulking, a notorious microbial issue in activated sludge plants, is always accompanied by dramatic changes in the bacterial community. Despite large numbers of phages in sludge systems, their responses to sludge bulking and phage-host associations during bulking are unknown. In this study, high-throughput sequencing of viral metagenomes and bacterial 16S rRNA genes were employed to characterize viral and bacterial communities in a sludge plant under different sludge conditions (sludge volume index (SVI) of 180, 132, and 73 ml/g). Bulking sludges (SVI > 125 ml/g) taken about 10 months apart exhibited similar bacterial and viral composition. This reflects ecological resilience of the sludge microbial community and indicates that changes in viral and bacterial populations correlate closely with each other. Overgrowth of "Candidatus Microthrix parvicella" led to filamentous bulking, but few corresponding viral genotypes were identified. In contrast, sludge viromes were characterized by numerous contigs associated with "Candidatus Accumulibacter phosphatis," suggesting an abundance of corresponding phages in the sludge viral community. Notably, while nitrifiers (mainly Nitrosomonadaceae and Nitrospiraceae) declined significantly along with sludge bulking, their corresponding viral contigs were identified more frequently and with greater abundance in the bulking viromes, implying that phage-mediated lysis might contribute to the loss of autotrophic nitrifiers under bulking conditions.

Improved genome recovery and integrated cell-size analyses of individual uncultured microbial cells and viral particles

Microbial single-cell genomics can be used to provide insights into the metabolic potential, interactions, and evolution of uncultured microorganisms. Here we present WGA-X, a method based on multiple displacement amplification of DNA that utilizes a thermostable mutant of the phi29 polymerase. WGA-X enhances genome recovery from individual microbial cells and viral particles while maintaining ease of use and scalability. The greatest improvements are observed when amplifying high G+C content templates, such as those belonging to the predominant bacteria in agricultural soils. By integrating WGA-X with calibrated index-cell sorting and high-throughput genomic sequencing, we are able to analyze genomic sequences and cell sizes of hundreds of individual, uncultured bacteria, archaea, protists, and viral particles, obtained directly from marine and soil samples, in a single experiment. This approach may find diverse applications in microbiology and in biomedical and forensic studies of humans and other multicellular organisms.

Single-cell genomics can be used to study uncultured microorganisms. Here, Stepanauskas et al. present a method combining improved multiple displacement amplification and FACS, to obtain genomic sequences and cell size information from uncultivated microbial cells and viral particles in environmental samples.

Excess of non-conservative amino acid changes in marine bacterioplankton lineages with reduced genomes

Surface ocean waters are dominated by planktonic bacterial lineages with highly reduced genomes. The best examples are the cyanobacterial genus Prochlorococcus, the alphaproteobacterial clade SAR11 and the gammaproteobacterial clade SAR86, which together represent over 50% of the cells in surface oceans. Several studies have identified signatures of selection on these lineages in today's ocean and have postulated selection as the primary force throughout their evolutionary history. However, massive loss of genomic DNA in these lineages often occurred in the distant past, and the selective pressures underlying these ancient events have not been assessed. Here, we probe ancient selective pressures by computing %GC-corrected rates of conservative and radical nonsynonymous nucleotide substitutions. Surprisingly, we found an excess of radical changes in several of these lineages in comparison to their relatives with larger genomes. Furthermore, analyses of allelic genome sequences of several populations within these lineages consistently supported that radical replacements are more likely to be deleterious than conservative changes. Our results suggest coincidence of massive genomic DNA losses and increased power of genetic drift, but we also suggest that additional evidence independent of the nucleotide substitution analyses is needed to support a primary role of genetic drift driving ancient genome reduction of marine bacterioplankton lineages.

Letting go: bacterial genome reduction solves the dilemma of adapting to predation mortality in a substrate-restricted environment

Resource limitation and predation mortality are major determinants of microbial population dynamics, and optimization for either aspect is considered to imply a trade-off with respect to the other. Adaptation to these selective factors may, moreover, lead to disadvantages at rich growth conditions. We present an example of a concomitant evolutionary optimization to both, substrate limitation and predation in an aggregate-forming freshwater bacterial isolate, and we elucidate an underlying genomic mechanism. Bacteria were propagated in serial batch culture in a nutrient-restricted environment either with or without a bacterivorous flagellate. Strains isolated after 26 growth cycles of the predator-prey co-cultures formed as much total biomass as the ancestor at ancestral growth conditions, albeit largely reallocated to cell aggregates. A ~273 kbp genome fragment was lost in three strains that had independently evolved with predators. These strains had significantly higher growth yield on substrate-restricted media than others that were isolated from the same treatment before the excision event. Under predation pressure, the isolates with the deletion outcompeted both, the ancestor and the strains evolved without predators even at rich growth conditions. At the same time, genome reduction led to a growth disadvantage in the presence of benzoate due to the loss of the respective degradation pathway, suggesting that niche constriction might be the price for the bidirectional optimization.

The Evolution of Bacterial Genome Architecture

The genome architecture of bacteria and eukaryotes evolves in opposite directions when subject to genetic drift, a difference that can be ascribed to the fact that bacteria exhibit a mutational bias that deletes superfluous sequences, whereas eukaryotes are biased toward large insertions. Expansion of eukaryotic genomes occurs through the addition of non-functional sequences, such as repetitive sequences and transposable elements, whereas variation in bacterial genome size is largely due to the acquisition and loss of functional accessory genes. These properties create the situation in which eukaryotes with very similar numbers of genes can have vastly different genome sizes, while in bacteria, gene number scales linearly with genome size. Some bacterial genomes, however, particularly those of species that undergo bottlenecks due to recent association with hosts, accumulate pseudogenes and mobile elements, conferring them a low gene content relative to their genome size. These non-functional sequences are gradually eroded and eliminated after long-term association with hosts, with the result that obligate symbionts have the smallest genomes of any cellular organism. The architecture of bacterial genomes is shaped by complex and diverse processes, but for most bacterial species, genome size is governed by a non-adaptive process, i.e., genetic drift coupled with a mutational bias toward deletions. Thus, bacteria with small effective population sizes typically have the smallest genomes. Some marine bacteria counter this near-universal trend: despite having immense population sizes, selection, not drift, acts to reduce genome size in response to metabolic constraints in their nutrient-limited environment.