Exploring Microdiversity in Novel Kordia sp. (Bacteroidetes) with Proteorhodopsin from the Tropical Indian Ocean via Single Amplified Genomes

A bloom of a single bacterium shapes the microbiome during outdoor diatom cultivation collapse

Algae-dominated ecosystems are fundamentally influenced by their microbiome. We lack information on the identity and function of bacteria that specialize in consuming algal-derived dissolved organic matter in high algal density ecosystems such as outdoor algal ponds used for biofuel production. Here, we describe the metagenomic and metaproteomic signatures of a single bacterial strain that bloomed during a population-wide crash of the diatom, Phaeodactylum tricornutum, grown in outdoor ponds. 16S rRNA gene data indicated that a single Kordia sp. strain (family Flavobacteriaceae) contributed up to 93% of the bacterial community during P. tricornutum demise. Kordia sp. expressed proteins linked to microbial antagonism and biopolymer breakdown, which likely contributed to its dominance over other microbial taxa during diatom demise. Analysis of accompanying downstream microbiota (primarily of the Rhodobacteraceae family) provided evidence that cross-feeding may be a pathway supporting microbial diversity during diatom demise. In situ and laboratory data with a different strain suggested that Kordia was a primary degrader of biopolymers during algal demise, and co-occurring Rhodobacteraceae exploited degradation molecules for carbon. An analysis of 30 Rhodobacteraceae metagenome assembled genomes suggested that algal pond Rhodobacteraceae commonly harbored pathways to use diverse carbon and energy sources, including carbon monoxide, which may have contributed to the prevalence of this taxonomic group within the ponds. These observations further constrain the roles of functionally distinct heterotrophic bacteria in algal microbiomes, demonstrating how a single dominant bacterium, specialized in processing senescing or dead algal biomass, shapes the microbial community of outdoor algal biofuel ponds.IMPORTANCEAquatic biogeochemical cycles are dictated by the activity of diverse microbes inhabiting the algal microbiome. Outdoor biofuel ponds provide a setting analogous to aquatic algal blooms, where monocultures of fast-growing algae reach high cellular densities. Information on the microbial ecology of this setting is lacking, and so we employed metagenomics and metaproteomics to understand the metabolic roles of bacteria present within four replicated outdoor ponds inoculated with the diatom Phaeodactylum tricornutum. Unexpectedly, after 29 days of cultivation, all four ponds crashed concurrently with a "bloom" of a single taxon assigned to the Kordia bacterial genus. We assessed how this dominant taxon influenced the chemical and microbial fate of the ponds following the crash, with the hypothesis that it was primarily responsible for processing senescent/dead algal biomass and providing the surrounding microbiota with carbon. Overall, these findings provide insight into the roles of microbes specialized in processing algal organic matter and enhance our understanding of biofuel pond microbial ecology.

Actinorhodopsin: an efficient and robust light-driven proton pump for bionanotechnological applications

Actinorhodopsins are encoded by a distinct group of microbial rhodopsin (MR) genes predominant in non-marine actinobacteria. Despite their role in the global energy cycle and potential for bionanotechnological applications, our understanding of actinorhodopsin proteins is limited. Here, we characterized the actinorhodopsin RlActR from the freshwater actinobacterium Rhodoluna lacicola, which conserves amino acid residues critical for light-driven proton pumping found in MRs. RlActR was efficiently overexpressed in Escherichia coli in milligram amounts and isolated with high purity and homogeneity. The purified RlActR absorbed green light and its primary proton acceptor exhibited a mildly acidic apparent pKa. Size-exclusion chromatography of RlActR purified in the relatively mild and harsh detergents 5-cyclohexyl-1-pentyl-β-D-maltoside and n-octyl-β-D-glucopyranoside revealed highly homogeneous oligomers and no disruption into monomers, indicating significant robustness of the RlActR oligomer. Cryo-electron microscopy and 2D classification of protein particles provided a projection structure identifying the oligomeric state of RlActR as a pentamer. Efficient establishment of a proton gradient across lipid membranes upon light illumination was demonstrated using RlActR-overexpressing E. coli cells and reconstituted RlActR proteoliposomes. In summary, these features make RlActR an attractive energizing building block for the bottom-up assembly of molecular systems for bionanotechnological applications.

Microbial diversity and biogeochemical cycling potential in deep-sea sediments associated with seamount, trench, and cold seep ecosystems

Due to their extreme water depths and unique physicochemical conditions, deep-sea ecosystems develop uncommon microbial communities, which play a vital role in biogeochemical cycling. However, the differences in the compositions and functions of the microbial communities among these different geographic structures, such as seamounts (SM), marine trenches (MT), and cold seeps (CS), are still not fully understood. In the present study, sediments were collected from SM, MT, and CS in the Southwest Pacific Ocean, and the compositions and functions of the microbial communities were investigated by using amplicon sequencing combined with in-depth metagenomics. The results revealed that significantly higher richness levels and diversities of the microbial communities were found in SM sediments, followed by CS, and the lowest richness levels and diversities were found in MT sediments. Acinetobacter was dominant in the CS sediments and was replaced by Halomonas and Pseudomonas in the SM and MT sediments. We demonstrated that the microbes in deep-sea sediments were diverse and were functionally different (e.g., carbon, nitrogen, and sulfur cycling) from each other in the seamount, trench, and cold seep ecosystems. These results improved our understanding of the compositions, diversities and functions of microbial communities in the deep-sea environment.

The microbial rare biosphere: current concepts, methods and ecological principles

Our ability to describe the highly diverse pool of low abundance populations present in natural microbial communities is increasing at an unprecedented pace. Yet we currently lack an integrative view of the key taxa, functions and metabolic activity which make-up this communal pool, usually referred to as the 'rare biosphere', across the domains of life. In this context, this review examines the microbial rare biosphere in its broader sense, providing an historical perspective on representative studies which enabled to bridge the concept from macroecology to microbial ecology. It then addresses our current knowledge of the prokaryotic rare biosphere, and covers emerging insights into the ecology, taxonomy and evolution of low abundance microeukaryotic, viral and host-associated communities. We also review recent methodological advances and provide a synthetic overview on how the rare biosphere fits into different conceptual models used to explain microbial community assembly mechanisms, composition and function.

Genome characteristics of Kordia antarctica IMCC3317T and comparative genome analysis of the genus Kordia

The genus Kordia is one of many genera affiliated with the family Flavobacteriaceae of the phylum Bacteroidetes, well known for its degradation of high molecular weight organic matters. The genus Kordia currently comprises eight species, type strains of which have been isolated from a diverse range of marine environments. As of this report, four genome sequences have been submitted for cultured strains of Kordia, but none are complete nor have they been analyzed comprehensively. In this study, we report the complete genome of Kordia antarctica IMCC3317^T, isolated from coastal seawater off the Antarctic Peninsula. The complete genome of IMCC3317^T consists of a single circular chromosome with 5.5 Mbp and a 33.2 mol% of G+C DNA content. The IMCC3317^T genome showed features typical of chemoheterotrophic marine bacteria and similar to other Kordia genomes, such as complete gene sets for the Embden–Meyerhof–Parnas glycolysis pathway, tricarboxylic acid cycle and oxidative phosphorylation. The genome also encoded many carbohydrate-active enzymes, some of which were clustered into approximately seven polysaccharide utilization loci, thereby demonstrating the potential for polysaccharide utilization. Finally, a nosZ gene encoding nitrous oxide reductase, an enzyme that catalyzes the reduction of N₂O to N₂ gas, was also unique to the IMCC3317^T genome.

Tara Oceans: towards global ocean ecosystems biology

A planetary-scale understanding of the ocean ecosystem, particularly in light of climate change, is crucial. Here, we review the work of Tara Oceans, an international, multidisciplinary project to assess the complexity of ocean life across comprehensive taxonomic and spatial scales. Using a modified sailing boat, the team sampled plankton at 210 globally distributed sites at depths down to 1,000 m. We describe publicly available resources of molecular, morphological and environmental data, and discuss how an ecosystems biology approach has expanded our understanding of plankton diversity and ecology in the ocean as a planetary, interconnected ecosystem. These efforts illustrate how global-scale concepts and data can help to integrate biological complexity into models and serve as a baseline for assessing ecosystem changes and the future habitability of our planet in the Anthropocene epoch.

Ecological and functional capabilities of an uncultured Kordia sp

Cultivable bacteria represent only a fraction of the diversity in microbial communities. However, the official procedures for classification and characterization of a novel prokaryotic species still rely on isolates. Nevertheless, due to single cell genomics, it is possible to retrieve genomes from environmental samples by sequencing them individually, and to assign specific genes to a specific taxon, regardless of their ability to grow in culture. In this study, a complete description was performed for uncultured Kordia sp. TARA_039_SRF, a proposed novel species within the genus Kordia, using culture-independent techniques. The type material was a high-quality draft genome (94.97% complete, 4.65% gene redundancy) co-assembled using ten nearly identical single amplified genomes (SAGs) from surface seawater in the North Indian Ocean during the Tara Oceans Expedition. The assembly process was optimized to obtain the best possible assembly metrics and a less fragmented genome. The closest relative of the species was Kordia periserrulae, which shared 97.56% similarity of the 16S rRNA gene, 75% orthologs and 89.13% average nucleotide identity. The functional potential of the proposed novel species included proteorhodopsin, the ability to incorporate nitrate, cytochrome oxidases with high affinity for oxygen, and CAZymes that were unique features within the genus. Its abundance at different depths and size fractions was also evaluated together with its functional annotation, revealing that its putative ecological niche could be particles of phytoplanktonic origin. It could putatively attach to these particles and consume them while sinking to the deeper and oxygen depleted layers of the North Indian Ocean.