Type strains of the genus Porphyrobacter belonging to the family Erythrobacteraceae and the class Alphaproteobacteria have been isolated from various environments, such as swimming pools, lake water and hot springs. P. cryptus DSM 12079T and P. tepidarius DSM 10594T out of all Erythrobacteraceae type strains, are two type strains that have been isolated from geothermal environments. Next-generation sequencing (NGS) technology offers a convenient approach for detecting situational types based on protein sequence differences between thermophiles and mesophiles; amino acid substitutions can lead to protein structural changes, improving the thermal stabilities of proteins. Comparative genomic studies have revealed that different thermal types exist in different taxa, and few studies have been focused on the class Alphaproteobacteria, especially the family Erythrobacteraceae. In this study, eight genomes of Porphyrobacter strains were compared to elucidate how Porphyrobacter thermophiles developed mechanisms to adapt to thermal environments. P. cryptus DSM 12079T grew optimally at 50 °C, which was higher than the optimal growth temperature of other Porphyrobacter type strains. Phylogenomic analysis of the genus Porphyrobacter revealed that P. cryptus DSM 12079T formed a distinct and independent clade. Comparative genomic studies uncovered that 1405 single-copy genes were shared by Porphyrobacter type strains. Alignments of single-copy proteins showed that various types of amino acid substitutions existed between P. cryptus DSM 12079T and the other Porphyrobacter strains. The primary substitution types were changes from glycine/serine to alanine. P. cryptus DSM 12079T was the sole thermophile within the genus Porphyrobacter. Phylogenomic analysis and amino acid frequencies indicated that amino acid substitutions might play an important role in the thermophily of P. cryptus DSM 12079T. Bioinformatic analysis revealed that major amino acid substitutional types, such as changes from glycine/serine to alanine, increase the frequency of α-helices in proteins, promoting protein thermostability in P. cryptus DSM 12079T. Hence, comparative genomic analysis broadens our understanding of thermophilic mechanisms in the genus Porphyrobacter and may provide a useful insight in the design of thermophilic enzymes for agricultural, industrial and medical applications.

Bacterial communities in sediments of the Caiwei Seamount, a typical guyot located in the northwest Pacific Ocean, were investigated. A total of 727,879 16S ribosomal RNA gene sequences were retrieved from eight sediment samples of the top (mean depth = 1,407 m) and the base (mean depth = 5,525 m) of the guyot through pyrosequencing of V6 hypervariable region and clustered into 32,844 operational taxonomic units. Abundant‐weighted UniFrac metric partitioned bacterial assemblies into two categories (the top community and the base community) by principal coordinates analysis, consisting with the grouping of sampling stations by environmental variables. Differences in depth and physicochemical properties of the surrounding environment (e.g., concentrations of dissolved oxygen and geochemical elements) between the top and the base of the guyot may cause this partition of bacterial communities, whereas the typical fluid flow around the guyot may potentially contribute to the bacterial dispersal and environmental homogeneity along the same layer, resulting in the similarity of bacterial community structure within the same region (the top or the base). The surface sediment on the top of the guyot harbored the bacterial communities with greater diversity and evenness, represented by Gamma‐ and Deltaproteobacteria involved in sulfur cycling. At the base of the guyot, Gammaproteobacteria related to sulfur‐oxidizing and Chloroflexi functioning in the decomposition of refractory organic matter dominated, suggesting that the redox condition at the interface of the sediment and the water can influence bacteria‐mediated elemental cycling, eventually shaping the physicochemical and geological characteristics of a guyot.

Most studies on the genesis of polymetallic nodules suggested that nodules in the South China Sea (SCS) are hydrogenetic; however, the complexity and the heterogeneity in hydrology and geochemistry of the SCS might cause different processes of nodule formation, impacting their application and economic value. Microbial-mediated ferromanganese deposition is an important process in nodule formation, but the related microbial potentials are still unclear in the SCS. In this study, we sampled in three typical regions (A, B, and C) of the SCS enriched with polymetallic nodules. Firstly, we investigated environmental and microbial characteristics of the water columns to determine the heterogeneity of upper seawater that directly influenced deep-sea environments. Then, microbial compositions and structures in sediment cores, overlying waters, and nodules (inside and outside) collected within the same region were analyzed for inferring features of nodule environments. Microbial interactions between nodules and surrounding environments were estimated with collinear network analysis. The microbial evidence indicated that geochemical characteristics in deep sea of the SCS that were key to the polymetallic nodule formation were severely affected by organic matter flux from upper water column. The sediment in region A was sub-oxic due to the large input of terrigenous and phytoplankton-derived organic matter, potentially enhancing the overflow of reduced metals from the porewater. The intense microbial interaction between nodules and surface sediment reinforced the origin of metals for the ferromanganese deposition from the sediment (diagenetic type). Contrarily, the sediments in regions B and C were relatively rich in oxygen, and metal ions could be majorly supplied from seawater (hydrogenetic type). The large discrepancy in microbial communities between nodule inside and remaining samples suggested that nodules experienced a long-term formation process, consistent with the feature of hydrogenetic nodules. Overall, distributions and interactions of microbial communities in nodules and surrounding environments significantly contributed to the nodule formation in the SCS by manipulating biogeochemical processes that eventually determined the source and the fate of metal ions.

Ammonia-oxidizing archaea (AOA) and bacteria (AOB), nitrite-oxidizing bacteria (NOB), and complete ammonia oxidizers (comammox) are responsible for nitrification in nature; however, some groups have been reported to utilize labile-dissolved organic nitrogen (LDON) for satisfying nitrogen demands. To understand the universality of their capacity of LDON metabolism, we collected 70 complete genomes of AOA, AOB, NOB, and comammox from typical environments for exploring their potentials in the metabolism of representative LDON (urea, polyamines, cyanate, taurine, glycine betaine, and methylamine). Genomic analyses showed that urea was the most popular LDON used by nitrifiers. Each group harbored unique urea transporter genes (AOA: dur3 and utp, AOB: utp, and NOB and comammox: urtABCDE and utp) accompanied by urease genes ureABC. The differentiation in the substrate affinity of these transporters implied the divergence of urea utilization efficiency in nitrifiers, potentially driving them into different niches. The cyanate transporter (cynABD and focA/nirC) and degradation (cynS) genes were detected mostly in NOB, indicating their preference for a wide range of nitrogen substrates to satisfy high nitrogen demands. The lack of genes involved in the metabolism of polyamines, taurine, glycine betaine, and methylamines in most of nitrifiers suggested that they were not able to serve as a source of ammonium, only if they were degraded or oxidized extracellularly as previously reported. The phylogenetic analyses assisted with comparisons of GC% and the Codon Adaptation Index between target genes and whole genomes of nitrifiers implied that urea metabolic genes dur3 and ureC in AOA evolved independently from bacteria during the transition from Thaumarchaeota to AOA, while utp in terrestrial AOA was acquired from bacteria via lateral gene transfer (LGT). Cyanate transporter genes cynS and focA/nirC detected only in a terrestrial AOA Candidadus Nitrsosphaera gargensis Ga9.2 could be gained synchronously with Nitrospira of NOB by an ancient LGT. Our results indicated that LDON utilization was a common feature in nitrifiers, but metabolic potentials were different among nitrifiers, possibly being intensely interacted with their niches, survival strategies, and evolutions.