Microbes in marine sediments represent a large portion of the biosphere, and resolving their ecology is crucial for understanding global ocean processes. Single-gene diversity surveys have revealed several uncultured lineages that are widespread in ocean sediments and whose ecological roles are unknown, and advancements in the computational analysis of increasingly large genomic data sets have made it possible to reconstruct individual genomes from complex microbial communities. Using these metagenomic approaches to characterize sediments is transforming our view of microbial communities on the ocean floor and the biodiversity of the planet. In recent years, marine sediments have been a prominent source of new lineages in the tree of life. The incorporation of these lineages into existing phylogenies has revealed that many belong to distinct phyla, including archaeal phyla that are advancing our understanding of the origins of cellular complexity and eukaryotes. Detailed comparisons of the metabolic potentials of these new lineages have made it clear that uncultured bacteria and archaea are capable of mediating key previously undescribed steps in carbon and nutrient cycling. Expected final online publication date for the Annual Review of Marine Science, Volume 13 is January 3, 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

O xygen (O 2 ), the second most abundant gas in the atmosphere on Earth, plays a critical role in nature, including aquatic environments. As the most favorable electron acceptor, O 2 drives the degradation of organic matter and influences the cycling of other elements (e.g., nitrogen, sulfur, phosphorus) (1). For decades, aerobic respiration has been studied by different methods in various environments (2-4). Due to the limit of detection by traditional methods (Winkler methods and methods that use electrochemical sensors and optodes), the measurement of respiratory activity in low-O 2 environments, such as oceanic oxygenminimum zones (OMZs), is rare (5), and even in fully oxygenated waters, the direct measurement of oxygen dynamics is difficult and the more indirect method of measurement of formazan formation has therefore been applied (6). The lack of detailed data on aerobic respiration in low-O 2 environments restricts the understanding of carbon budgets (7) and the prediction of the development of O 2 within such environments (8). Recently, STOX oxygen sensors have been applied to quantify O 2 respiration rates in OMZs (9), and by this technique, it was possible to measure rates down to about 1 nmol Ϫ1 liter Ϫ1 h Ϫ1 , which is a level of resolution that is a factor of 10 higher than that obtained by traditional methods (10). Half-saturation constants (apparent K m values) for microbial communities were estimated from the data obtained with STOX oxygen sensors, but highly variable values ranging from 30 to 200 nmol liter Ϫ1 were obtained. Another study indicated high half-saturation O 2 concentrations of several micromolar, supposedly caused by diffusion limitation around and within aggregates (11).The final step of aerobic respiration is conducted by a terminal cytochrome oxidase, a membrane-associated protein which transfers electrons to O 2 (12). Two main families of terminal oxidases have been classified on the basis of structural and functional differences (13-16): the heme-copper oxidases (HCOs) and the cytochrome bd-type oxidases. Furthermore, three classes have been identified within HCOs according to the combination of different heme subunits (classes A, B, and C). The kinetic parameters maximum respiration rate (V max ) and K m can be used to describe respiratory activity as a function of the O 2 concentration, although it should be kept in mind that the Michaelis-Menten equation strictly applies only to the kinetics of single enzymes. According to the affinity of O 2 , these terminal oxidases can be classified as high-affinity terminal oxidases (with K m values of about 3 to 8 nmol liter Ϫ1 ) (17) and low-affinity terminal oxidases (with K m values of about 200 nmol liter Ϫ1 ) (18). Respiration rates in aquatic environments have been estimated by different methods, and the kinetics have been estimated using several models. Different equations have been proposed to estimate V max and K m values, such as fitting of the data directly to the Michaelis-Menten equation by computer-aided iterative regres...

Strain S3-2T, isolated from sediment of a frozen freshwater pond, shares 99% 16S rRNA gene sequence identity with strains of the genus Janthinobacterium. Strain S3-2T is a facultative anaerobe that lacks the ability to produce violacein but shows antibiotic resistance, psychrotolerance, incomplete denitrification, and fermentation. The draft genome of strain S3-2T has a size of ~5.8 Mbp and contains 5,297 genes, including 115 RNA genes. Based on the phenotypic properties of the strain, the low in silico DNA-DNA hybridization (DDH) values with related genomes (<35%), and the low whole genome-based average nucleotide identity (ANI) (<86%) with other strains within the genus Janthinobacterium, we propose that strain S3-2T is the type strain (= DSM 102223 = LMG 29653) of a new species within this genus. We propose the name Janthinobacterium psychrotolerans sp. nov. to emphasize the capability of the strain to grow at low temperatures.Electronic supplementary materialThe online version of this article (doi:10.1186/s40793-017-0230-x) contains supplementary material, which is available to authorized users.

DPANN are small-celled archaea that are generally predicted to be symbionts, and in some cases are known episymbionts of other archaea. As the monophyly of the DPANN remains uncertain, we hypothesized that proteome content could reveal relationships among DPANN lineages, constrain genetic overlap with bacteria, and illustrate how organisms with hybrid bacterial and archaeal protein sets might function. We tested this hypothesis using protein family content that was defined in part using 3,197 genomes including 569 newly reconstructed genomes. Protein family content clearly separates the final set of 390 DPANN genomes from other archaea, paralleling the separation of Candidate Phyla Radiation (CPR) bacteria from all other bacteria. This separation is partly driven by hypothetical proteins, some of which may be symbiosis-related. Pacearchaeota with the most limited predicted metabolic capacities have Form II/III and III-like Rubisco, suggesting metabolisms based on scavenged nucleotides. Intriguingly, the Pacearchaeota and Woesearchaeota with the smallest genomes also tend to encode large extracellular murein-like lytic transglycosylase domain proteins that may bind and degrade components of bacterial cell walls, indicating that some might be episymbionts of bacteria. The pathway for biosynthesis of bacterial isoprenoids is widespread in Woesearchaeota genomes and is encoded in proximity to genes involved in bacterial fatty acids synthesis. Surprisingly, in some DPANN genomes we identified a pathway for synthesis of queuosine, an unusual nucleotide in tRNAs of bacteria. Other bacterial systems are predicted to be involved in protein refolding. For example, many DPANN have the complete bacterial DnaK-DnaJ-GrpE system and many Woesearchaeota and Pacearchaeota possess bacterial group I chaperones. Thus, many DPANN appear to have mechanisms to ensure efficient protein folding of both archaeal and laterally acquired bacterial proteins.

The final step of aerobic respiration is carried out by a terminal oxidase transporting electrons to oxygen (O2). Prokaryotes harbor diverse terminal oxidases that differ in phylogenetic origin, structure, biochemical function, and affinity for O2. Here we report on the expression of high-affinity (cytochrome cbb3 oxidase), low-affinity (cytochrome aa3 oxidase), and putative low-affinity (cyanide-insensitive oxidase (CIO)) terminal oxidases in the marine bacteria Idiomarina loihiensis L2-TR and Marinobacter daepoensis SW-156 upon transition to very low O2 concentrations (<200 nM), measured by RT-qPCR. In both strains, high-affinity cytochrome cbb3 oxidase showed the highest expression levels and was significantly up-regulated upon transition to low O2 concentrations. Low-affinity cytochrome aa3 oxidase showed very low transcription levels throughout the incubation. Surprisingly, however, it was also up-regulated upon transition to low O2 concentrations. In contrast, putative low-affinity CIO had much lower expression levels and markedly different regulation patterns between the two strains. These results demonstrate that exposure to low O2 concentrations regulates the gene expression of different types of terminal oxidases, but also that the type and magnitude of transcriptional response is species-dependent. Therefore, in situ transcriptome data cannot, without detailed knowledge of the transcriptional regulation of the species involved, be translated into relative respiratory activity.

No abstract

The Indian Ocean is characterized by its complex physical systems and strong seasonal monsoons. To better understand effects of seasonal monsoon-driven circulation on the bacterioplanktonic community structure in surface waters and the bacterial distribution response to vertical stratification, patterns of seasonal, and vertical distribution of bacterial communities in the Eastern Tropical Indian Ocean were investigated using 16S rRNA gene profiling. Water samples were collected during the Southwest monsoon (from June to August), the fall inter-monsoon (from October and November) and the Northeast monsoon (from December to January), respectively, onboard during three cruises from July 2016 to January 2018. Surface bacterioplankton communities in these three seasons and in the upper water (3–300 m with six depths) during the Northeast monsoon contained a diverse group of taxa, mainly Proteobacteria, Cyanobacteria, Actinobacteria, Bacteroidetes, and Chloroflexi. Redundancy discriminant analysis (RDA) uncovered that temperature, salinity, and dissolved oxygen (DO) were crucial environmental parameters that affected the structure of bacterial community in overall surface samples. However, significant differences in the composition of the bacterial community are likely due to changes in concentrations of salinity during the fall inter-monsoon, while phosphate for both the Southwest monsoon and the Northeast monsoon. Pearson's analysis revealed that the seasonal variation rather than the vertical variation of environmental factors had a more significant impact on the composition of bacterial community. In addition, a clear seasonal pattern of bacterial co-occurrence showed that inter-taxa associations during the fall inter-monsoon were closer than during the Northeast monsoon and the Southwest monsoon. Overall, our results implied clear differences in the composition of bacterial community, with more pronounced seasonal variation compared to the vertical variation in response to environmental changes.

DPANN are small-celled archaea that are generally predicted to be symbionts, and in some cases are known episymbionts of other archaea. As the monophyly of the DPANN remains uncertain, we hypothesized that proteome content could reveal relationships among DPANN lineages, constrain genetic overlap with bacteria, and illustrate how organisms with hybrid bacterial and archaeal protein sets might function. We tested this hypothesis using protein family content that was defined in part using 569 newly reconstructed genomes. Protein family content clearly separates DPANN from other archaea, paralleling the separation of Candidate Phyla Radiation (CPR) bacteria from all other bacteria. This separation is partly driven by hypothetical proteins, some of which may be symbiosis-related. Pacearchaeota with the most limited predicted metabolic capacities have Form II/III and III-like Rubisco, suggesting metabolisms based on scavenged nucleotides. Intriguingly, the Pacearchaeota and Woesearchaeota with the smallest genomes also tend to encode large extracellular murein-like lytic transglycosylase domain proteins that may bind and degrade components of bacterial cell walls, indicating that some might be episymbionts of bacteria. The pathway for biosynthesis of bacterial isoprenoids is widespread in Woesearchaeota genomes and is encoded in proximity to genes involved in bacterial fatty acids synthesis. Surprisingly, in some DPANN genomes we identified a pathway for synthesis of queuosine, an unusual nucleotide in tRNAs of bacteria. Other bacterial systems are predicted to be involved in protein refolding. For example, many DPANN have the complete bacterial DnaK-DnaJ-GrpE system and many Woesearchaeota and Pacearchaeota possess bacterial group I chaperones. Thus, many DPANN appear to have mechanisms to ensure efficient protein folding of both archaeal and laterally acquired bacterial proteins.