Cultivation of marine bacteria of the SAR202 clade

Earth's most needed uncultivated aquatic prokaryotes

Aquatic ecosystems house a significant fraction of Earth's biosphere, yet most prokaryotes inhabiting these environments remain uncultivated. While recently developed genome-resolved metagenomics and single-cell genomics techniques have underscored the immense genetic breadth and metabolic potential residing in uncultivated Bacteria and Archaea, cultivation of these microorganisms is required to study their physiology via genetic systems, confirm predicted biochemical pathways, exploit biotechnological potential, and accurately appraise nutrient turnover. Over the past two decades, the limitations of culture-independent investigations highlighted the importance of cultivation in bridging this vast knowledge gap. Here, we collected more than 80 highly sought-after uncultivated lineages of aquatic Bacteria and Archaea with global ecological impact. In addition to fulfilling critical roles in global carbon, nitrogen, and sulfur cycling, many of these organisms are thought to partake in key symbiotic relationships. This review highlights the vital contributions of uncultured microbes in aquatic ecosystems, from lakes and groundwater to the surfaces and depths of the oceans and will guide current and future initiatives tasked with cultivating our planet's most elusive, yet highly consequential aquatic microflora.

Genome-streamlined SAR202 bacteria are widely present and active in the euphotic ocean

SAR202 bacteria are a diverse group of bacteria in the ocean. The SAR202 lineages dominate the bacterial community and evolve specialized metabolisms for oxidizing recalcitrant organic compounds in the dark ocean. SAR202 bacteria are also present in the euphotic oceans; however, their ecological roles and metabolic potential remain poorly understood. In this study, we collected 392 non-redundant metagenome-assembled genomes from different oceans, with 18% of these SAR202 genomes characterized by small genome sizes (<2 Mbp), low GC content (<40%), and high gene density. The 70 genome-streamlined SAR202 bacteria constitute more than an average of 90% of SAR202 in the euphotic zone and exhibit streamlined metabolic features compared to the dark ocean SAR202. Genome-streamlined SAR202 is distributed in many major SAR202 lineages (i.e. I, II, III, and VI). Phylogenomic analysis shows that the genome-streamlined SAR202 clades diverged from the non-genome-streamlined SAR202 lineages and evolved independently within the same clades. Certain genes are enriched in genome-streamlined SAR202, such as proteorhodopsin genes and the coding genes of major facilitator superfamily transporters, nucleoside transporters, and deoxyribodipyrimidine photo-lyase, indicating their adaptation to sunlit oligotrophic water. A detailed comparison between genome-streamlined SAR202 and non-genome-streamlined SAR202 was made to illustrate their distinct niche distribution and metabolic buildup. In addition, the metatranscriptomic analysis supports that genome-streamlined SAR202 bacteria are active in the upper ocean. This study represents a systematic study of streamlined SAR202 bacteria that occupy the euphotic ocean and provides a comprehensive view of the ecological roles of SAR202 bacteria in the ocean.

Leuconostoc aquikimchii sp. nov., a Lactic Acid Bacterium Isolated from Cabbage Watery Kimchi

Two Gram-stain-positive, facultatively anaerobic, non-hemolytic, coccoid-shaped bacterial strains, designated MS01T and MS02, were isolated from cabbage watery kimchi in the Republic of Korea. Cellular growth occurred at 5-25 ℃ (optimum, 20 ℃), pH 5-8 (optimum, pH 7) and in the presence of 0-5% (w/v) NaCl (optimum, 1%). Results of 16S rRNA gene-based phylogenetic analyses showed that strains MS01T and MS02 shared identical sequences, clustered within the Leuconostoc clade in phylogenetic trees, and were most closely related to Leuconostoc inhae IH003T and Leuconostoc gasicomitatum LMG 18811T with sequence similarities of 98.74%. The complete whole-genome sequences of strains MS01T and MS02 measured 2.04-2.06 Mbp and harbored a 50.6 kb plasmid, with DNA G + C contents of 37.7% for both. Based on average nucleotide identities (ANI) and digital DNA-DNA hybridization (dDDH) values, both strains were confirmed to belong to the same species but showed ≤ 85.9% ANI and ≤ 29.9% dDDH values to other Leuconostoc species, indicating that they represent a novel species. Metabolic pathway reconstruction revealed that both strains perform heterolactic acid fermentation, producing lactate, acetate, and ethanol. Chemotaxonomic analyses, including cellular fatty acids, polar lipids, and peptidoglycan amino acid, confirmed the inclusion of both strains within the genus Leuconostoc. Based on the phylogenetic, genomic, and phenotypic characterization, strains MS01T and MS02 were considered to represent a novel species within the genus Leuconostoc, for which the name Leuconostoc aquikimchii sp. nov. is proposed with MS01T (= KACC 23748T = JCM 37028T) as the type strain.

Taxonomic and functional partitioning of Chloroflexota populations under ferruginous conditions at and below the sediment-water interface

The adaptation of the phylum Chloroflexota to various geochemical conditions is thought to have originated in primitive microbial ecosystems, involving hydrogenotrophic energy conservation under ferruginous anoxia. Oligotrophic deep waters displaying anoxic ferruginous conditions, such as those of Lake Towuti, and their sediments may thus constitute a preferential ecological niche for investigating metabolic versatility in modern Chloroflexota. Combining pore water geochemistry, cell counts, sulfate reduction rates, and 16S rRNA genes with in-depth analysis of metagenome-assembled genomes, we show that Chloroflexota benefit from cross-feeding on metabolites derived from canonical respiration chains and fermentation. Detailing their genetic contents, we provide molecular evidence that Anaerolineae have metabolic potential to use unconventional electron acceptors, different cytochromes, and multiple redox metalloproteins to cope with oxygen fluctuations, and thereby effectively colonizing the ferruginous sediment-water interface. In sediments, Dehalococcoidia evolved to be acetogens, scavenging fatty acids, haloacids, and aromatic acids, apparently bypassing specific steps in carbon assimilation pathways to perform energy-conserving secondary fermentations combined with CO2 fixation via the Wood-Ljungdahl pathway. Our study highlights the partitioning of Chloroflexota populations according to alternative electron acceptors and donors available at the sediment-water interface and below. Chloroflexota would have developed analogous primeval features due to oxygen fluctuations in ancient ferruginous ecosystems.

Unveiling the microbial diversity across the northern Ninety East Ridge in the Indian Ocean

Prokaryotes play a crucial role in marine ecosystem health and drive biogeochemical processes. The northern Ninety East Ridge (NER) of the Indian Ocean, a pivotal yet understudied area for these cycles, has been the focus of our study. We employed high-throughput 16S rRNA gene sequencing to analyze 35 water samples from five stations along the ridge, categorized into three depth- and dissolved oxygen-level-based groups. Our approach uncovered a clear stratification of microbial communities, with key bioindicators such as Prochlorococcus MIT9313, Sva0996 marine group, and Candidatus Actinomarina in the upper layer; Ketobacter, Pseudophaeobacter, Nitrospina, and SAR324 clade in the middle layer; and Methylobacterium-Methylorubrum, Sphingomonas, Sphingobium, and Erythrobacter in the deep layer. Methylobacterium-Methylorubrum emerged as the most abundant bacterial genus, while Nitrosopumilaceae predominated among archaeal communities. The spatial and depth-wise distribution patterns revealed that Ketobacter was unique to the northern NER, whereas Methylobacterium-Methylorubrum, UBA10353, SAR324 clade, SAR406, Sva0996_marine_group, Candidatus Actinomarina were ubiquitous across various marine regions, exhibiting niche differentiation at the OTU level. Environmental factors, especially dissolved oxygen (DO), silicate, nitrate, and salinity, significantly influence community structure. These findings not only reveal the novelty and adaptability of the microbial ecosystem in the northern NER but also contribute to the broader understanding of marine microbial diversity and its response to environmental heterogeneity.

Deep metagenomic sequencing unveils novel SAR202 lineages and their vertical adaptation in the ocean

SAR202 bacteria in the Chloroflexota phylum are abundant and widely distributed in the ocean. Their genome coding capacities indicate their potential roles in degrading complex and recalcitrant organic compounds in the ocean. However, our understanding of their genomic diversity, vertical distribution, and depth-related metabolisms is still limited by the number of assembled SAR202 genomes. In this study, we apply deep metagenomic sequencing (180 Gb per sample) to investigate microbial communities collected from six representative depths at the Bermuda Atlantic Time Series (BATS) station. We obtain 173 SAR202 metagenome-assembled genomes (MAGs). Intriguingly, 154 new species and 104 new genera are found based on these 173 SAR202 genomes. We add 12 new subgroups to the current SAR202 lineages. The vertical distribution of 20 SAR202 subgroups shows their niche partitioning in the euphotic, mesopelagic, and bathypelagic oceans, respectively. Deep-ocean SAR202 bacteria contain more genes and exhibit more metabolic potential for degrading complex organic substrates than those from the euphotic zone. With deep metagenomic sequencing, we uncover many new lineages of SAR202 bacteria and their potential functions which greatly deepen our understanding of their diversity, vertical profile, and contribution to the ocean's carbon cycling, especially in the deep ocean.

Crystal structure of L-2-keto-3-deoxyfuconate 4-dehydrogenase reveals a unique binding mode as a α-furanosyl hemiketal of substrates

L-2-Keto-3-deoxyfuconate 4-dehydrogenase (L-KDFDH) catalyzes the NAD+-dependent oxidization of L-2-keto-3-deoxyfuconate (L-KDF) to L-2,4-diketo-3-deoxyfuconate (L-2,4-DKDF) in the non-phosphorylating L-fucose pathway from bacteria, and its substrate was previously considered to be the acyclic α-keto form of L-KDF. On the other hand, BDH2, a mammalian homolog with L-KDFDH, functions as a dehydrogenase for cis-4-hydroxy-L-proline (C4LHyp) with the cyclic structure. We found that L-KDFDH and BDH2 utilize C4LHyp and L-KDF, respectively. Therefore, to elucidate unique substrate specificity at the atomic level, we herein investigated for the first time the crystal structures of L-KDFDH from Herbaspirillum huttiense in the ligand-free, L-KDF and L-2,4-DKDF, D-KDP (D-2-keto-3-deoxypentonate; additional substrate), or L-2,4-DKDF and NADH bound forms. In complexed structures, L-KDF, L-2,4-DKDF, and D-KDP commonly bound as a α-furanosyl hemiketal. Furthermore, L-KDFDH showed no activity for L-KDF and D-KDP analogs without the C5 hydroxyl group, which form only the acyclic α-keto form. The C1 carboxyl and α-anomeric C2 hydroxyl groups and O5 oxygen atom of the substrate (and product) were specifically recognized by Arg148, Arg192, and Arg214. The side chain of Trp252 was important for hydrophobically recognizing the C6 methyl group of L-KDF. This is the first example showing the physiological role of the hemiketal of 2-keto-3-deoxysugar acid.

A pilot study suggests the correspondence between SAR202 bacteria and dissolved organic matter in the late stage of a year-long microcosm incubation

SAR202 bacteria are abundant in the marine environment and they have been suggested to contribute to the utilization of recalcitrant organic matter (RDOM) within the ocean's biogeochemical cycle. However, this functional role has only been postulated by metagenomic studies. During a one-year microcosm incubation of an open ocean microbial community with lysed Synechococcus and its released DOM, SAR202 became relatively more abundant in the later stage (after day 30) of the incubation. Network analysis illustrated a high degree of negative associations between SAR202 and a unique group of molecular formulae (MFs) in phase 2 (day 30 to 364) of the incubation, which is empirical evidence that SAR202 bacteria are major consumers of the more oxygenated, unsaturated, and higher-molecular-weight MFs. Further investigation of the SAR202-associated MFs suggested that they were potentially secondary products arising from initial heterotrophic activities following the amendment of labile Synechococcus-derived DOM. This pilot study provided a preliminary observation on the correspondence between SAR202 bacteria and more resistant DOM, further supporting the hypothesis that SAR202 bacteria play important roles in the degradation of RDOM and thus the ocean's biogeochemical cycle.

ACR: metagenome-assembled prokaryotic and eukaryotic genome refinement tool

Microbial genome recovery from metagenomes can further explain microbial ecosystem structures, functions and dynamics. Thus, this study developed the Additional Clustering Refiner (ACR) to enhance high-purity prokaryotic and eukaryotic metagenome-assembled genome (MAGs) recovery. ACR refines low-quality MAGs by subjecting them to iterative k-means clustering predicated on contig abundance and increasing bin purity through validated universal marker genes. Synthetic and real-world metagenomic datasets, including short- and long-read sequences, evaluated ACR's effectiveness. The results demonstrated improved MAG purity and a significant increase in high- and medium-quality MAG recovery rates. In addition, ACR seamlessly integrates with various binning algorithms, augmenting their strengths without modifying core features. Furthermore, its multiple sequencing technology compatibilities expand its applicability. By efficiently recovering high-quality prokaryotic and eukaryotic genomes, ACR is a promising tool for deepening our understanding of microbial communities through genome-centric metagenomics.