Intracellular biopolymers serve versatile functions, allowing microbes to adapt to fluctuating environmental conditions. The metabolic interdependence of dual biopolymers polyphosphate (polyP) and polyhydroxyalkanoates (PHA) is a defining feature of polyphosphate-accumulating organisms (PAOs), the key agents enabling enhanced biological phosphorus removal (EBPR). Beyond EBPR, PAOs accumulating both polyP and PHA (PHA-PAOs) in natural environments remain unexplored due to limited detection tools, despite hypothesized roles in nutrient cycling. This study presents a novel phenotype-targeted approach integrating triple-stained fluorescence-activated cell sorting with 16S rRNA gene sequencing (TriFlow-Seq) to detect, quantify, and phylogenetically characterize PHA-PAOs, validated by fluorescence imaging and single-cell Raman spectroscopy. TriFlow-Seq of EBPR samples confirmed known PAOs, including Candidatus Phosphoribacter, Tetrasphaera, and Ca. Accumulibacter, and revealed new candidate PHA-PAOs within the Rhodobacteraceae family. In maize rhizosphere, TriFlow-Seq led to the discovery of diverse PHA-PAOs, Pseudomonas, Halomonas, and Nannocystis. These genera participate in plant-growth-promoting functions including phosphate solubilization and phytohormone production, yet their simultaneous polyP and PHA accumulation has never been reported. Our findings revealed high PHA-PAO prevalence and distinct phylogenetic patterns associated with different maize genotypes, suggesting an overlooked role of biopolymer costorage in rhizosphere dynamics. This study establishes a pioneering approach to investigating PHA-PAO identities and roles across ecosystems.

Whole-genome draft assemblies of Paracoccus pantotrophus DSM 11073 and Paracoccus sp. AS002: Phylogenetics entails classification as Paracoccus versutus AS002.

This study investigated the effects of compound Chinese herbal medicine (CCHM) on nutrient digestibility, rumen fermentation parameters, and microbial structure in suckling lambs. Sixty Lambs born as twins (from the same ewe), each 8 days old, were randomly assigned to two groups. The control and treatment groups received 0 and 0.2% CCHM in the basal diet, respectively. Digestion experiments were conducted during the trial. Rumen fluid samples were collected from slaughtered lambs in the final week for microbiome analysis. The results indicated that average daily gain and average daily feed intake were significantly improved by CCHM. The apparent digestibility of dry matter and acid detergent fiber also increased significantly. CCHM supplementation elevated Ammonia nitrogen (NH3-N), total volatile fatty acids (TVFAs), acetate, and propionate concentrations in the rumen. The relative abundance of Firmicutes, Actinobacteria, Patescibacteria, Succiniclasticum, Selenomonas, Olsenella, and Shuttleworthia increased in the treatment group. Linear discriminant analysis Effect Size (LEfSe) revealed ten bacterial groups significantly enriched in the treatment group. These included Patescibacteria (Phylum), Negativicutes and Saccharimonadia (Class), Saccharimonadia and Rhodobacterales (Order), Saccharimonadiahe and Rhodobacteraceae (Family), and Prevotell-9, Saccharimonadales, and Limosilicobacillus (Genus). Thirteen CAZyme families were detected. Two enzyme families, GH34-5 and CBM4, were enriched in the control group, while eleven families were enriched in the treatment group: GT14, GH89, GH84, GH63, GH5-36, CBM58, PL37, GH85, GH165, GH110, and GH50. Correlation analysis between rumen bacteria, carbohydrate enzymes, and fermentation parameters showed a positive correlation between Saccharimonadales and GH63. Limosilactobacillus showed a positive correlation with CBM58. Negative correlations were found between Romboutsia and both GT14 and PL37. GH84, GH165, GH85, and GH50 were positively correlated with NH3-N concentration. CBM58, GT14, GH89, GH110, GH50, and PL37 showed positive associations with TVFAs. This study demonstrates that dietary supplementation with CCHM during the suckling period improves growth performance, enhances nutrient digestibility, increases rumen fermentation capacity, modulates microbial abundance, and promotes lamb development in Hu sheep.

While oligotrophic bacteria are known to dominate most marine microbial habitats, under certain conditions, such as during phytoplankton blooms, copiotrophs can dramatically increase in abundance and reach towering proportions of the bacterial communities. We are uncertain whether the bacteria exhibiting this capacity, which we denote as "bloomers," have specific functional characteristics or if, instead, they are randomly selected from the broader pool of copiotrophs. To explore the genomic determinants of this ecological trait, we conducted a comparative genomic analysis of bacterial genomes from microcosm experiments where grazer and viral presence was reduced and nutrient availability was increased, conditions that triggered bacterial blooms. We tested which functional genes were overrepresented in the bacteria that responded to the treatments, examining a total of 305 genomes from isolates and metagenome-assembled genomes (MAGs) that were categorized as copiotrophs or oligotrophs according to their codon usage bias (CUB). The responsive bacteria were enriched in genes related to transcriptional regulation in response to stimuli (mostly via two-component systems), transport, secretion, cell protection, catabolism of sugars and amino acids, and membrane/cell wall biosynthesis. These genes confer on them capabilities for adhesion, biofilm formation, resistance to stress, quorum sensing, chemotaxis, nutrient uptake, and fast replication. They were overrepresented mainly in copiotrophic genomes from the families Alteromonadaceae, Vibrionaceae, Rhodobacteraceae, Sphingomonadaceae, and Flavobacteriaceae. Additionally, we found that these responsive bacteria, when abundant, could affect biogeochemical cycling, particularly the phosphorus cycle. In this study, we provide insights into the functional characteristics that enable certain bacteria to rapidly respond to changes in the environment and bloom. We also hint at the ecological meaning and implications of these phenomena that could affect biogeochemical cycles in the oceans. Video Abstract.

Sea cucumbers are highly valued commercial species in the seafood industry. However, their hatchery and commercialization are constrained by the high mortalities experienced by these animals driven by environmental changes and physiological stress. Under such conditions, functional alterations in their immune system can induce integument ulcers that are later infected by opportunistic pathogens. Sea cucumbers, however, can display defense mechanisms that enable self-healing and recovery. It has been hypothesized that such mechanisms are assisted by changes in the skin-associated microbial community, enhancing the resilience of infected animal hosts. Here, we investigated the dynamics of the skin-associated microbiomes during infection and recovery of the tropical sea cucumber Holothuria scabra. Our findings reveal that the acclimation process for both, the host and the microbiome occurs simultaneously, with the latter gradually resembling the surrounding water environment after one month. The gradual healing of the sea cucumber skin and the structural changes in the associated microbiome were concurrent to the decline of pathogenic bacteria and the increase in the abundance of the family Rhodobacteraceae. The enrichment of some members from this group (genus Ruegeria) suggests a potential beneficial role in facilitating sea cucumber host recovery and acclimation. Our study provides valuable insights into the dynamics of the skin microbiome in sea cucumbers, highlighting the key role of this organismal trait for the resilience and overall health of the sea cucumber host.

Vertical transfer of bacterial symbionts via a placental analogue in the cyclostome bryozoan Patinella verrucaria (Stenolaemata): Ultrastructural and molecular evidence.

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.

Giant clams, with their significant ecological importance, depend on associated bacteria for their health and development, yet the transmission modes and succession of community dynamics of these bacteria remain poorly understood. This study employed 16S rRNA gene sequencing and microscopy to investigate the transmission and community dynamics of symbiotic bacteria in the giant clam Tridacna crocea during early developmental stages (fertilized eggs, blastocyst, D-larvae, and pediveliger larvae). Fluorescence in situ hybridization and transmission electron microscopy did not detect internal symbiotic bacteria in fertilized eggs and adult gonad gametes, but scanning electron microscopy revealed microbial structures on egg surface microvilli, suggesting their role as microbial carriers. 16S rRNA sequencing confirmed microbial presence in fertilized eggs, indicating bacterial acquisition via external vertical transmission (adherence to microvilli) or horizontal transmission. Given the lack of internalized bacteria in reproductive organs, we prefer to classify the symbiotic bacteria acquisition as horizontal transmission. Microbial community analysis showed that T. crocea acquired a significant portion of its microbiome from seawater throughout its development. Before reaching the pediveliger stage, the bacterial community composition closely resembled that of the surrounding seawater, primarily featuring the family Rhodobacteraceae. As T. crocea matured, the host's selective pressure increased (e.g. deterministic assembly), which simplified the microbial community and reduced diversity. During the pediveliger stage, the genus Endozoicomonas became dominant, forming a large proportion of the bacterial community within the gonads. This highlights the ecological significance of host-microbe interactions in maintaining biodiversity and driving ecosystem stability through dynamic community assembly processes.

The northwest Arabian Gulf encounters significant anthropogenic pressures, including nutrient enrichment from coastal development and effluent discharge. This study presents the first shotgun metagenomics-based characterization of microbial communities in Kuwaiti waters of the northwest Arabian Gulf, focusing on Kuwait's first Marine Protected Area (MPA) in Sulaibikhat Bay, a vital nursery ground for commercially important fish. Analysis revealed significantly higher microbial diversity within the MPA compared to adjacent waters, with Rhodobacteraceae (27.8%) and Flavobacteriaceae (15.3%) being dominant. Elevated inorganic phosphorus, nitrogen, and salinity were key factors driving this diversity. Multivariate analysis highlighted phosphate as a critical component affecting the MPA microbial community structure, particularly for the families Microbacteriaceae, Flavobacteriaceae, and Rhodobacteraceae. This study underscores the ecological importance of MPAs and highlights the impact of nutrient enrichment and other environmental stressors on microbial diversity, emphasizing the need to reduce nutrient influx to mitigate eutrophication and enhance marine ecosystem resilience in stressed environments.

Strain LCG007, isolated from Lu Chao Harbor's intertidal water, phylogenetically represents a novel genus within the family Rhodobacteraceae. Metabolically, it possesses a wide array of amino acid metabolic genes that enable it to thrive on both amino acids or peptides. Also, it could hydrolyze peptides containing D-amino acids, highlighting its potential role in the cycling of refractory organic matter. Moreover, strain LCG007 could utilize various carbohydrates, including mannopine and D-apiose-compounds primarily derived from terrestrial plants-demonstrating its capacity to degrade terrestrial organic matter. It could assimilate ammonia, nitrate and nitrite, and utilizes organic nitrogen sources such as polyamines, along with diverse organic and inorganic phosphorus and sulfur sources. Importantly, unlike very limited Sulfitobacter species that possess photosynthetic genes, the genomes of strain LCG007-affiliated genus and all Roseobacter species harbor photosynthetic gene clusters. This conservation was further supported by the significant impact of light on the growth and cell aggregation of strain LCG007, suggesting that acquirement of photosynthetic genes could play a crucial role in the speciation of their common ancestor. In terms of environmental adaptability, the genes that encode for DNA photolyase, heat and cold shock proteins, and enzymes responsible for scavenging reactive oxygen species, along with those involved in the uptake and biosynthesis of osmoprotectants such as betaine, γ-aminobutyric acid (GABA), and trehalose collectively enable strain LCG007 to survive in the dynamic and complex intertidal zone environment. Besides, the capacity in biofilm formation is crucial for its survival under conditions of oligotrophy or high salinity. This study enhances our comprehension of the microbial taxonomy within the Roseobacter clade affiliated cluster, their survival strategies in intertidal ecosystems, and underscores the significance of their role in nutrient cycling. It also highlights the crucial importance of photosynthetic metabolism for the speciation of marine bacteria and their ecological resilience.

Abstract Egg masses of Aplysia depilans consist of long and intertwined strings containing numerous capsules with eggs. Light microscopy stains and transmission electron microscopy revealed four layers in the gelatinous sheath that encircled and aggregated the chain of egg capsules. The outermost layer has a fluffy structure. The second, third, and fourth layers consisted of reticulated matrices with different densities. The second and third layers were divided into 5‒6 strata each. The fourth and innermost layer of the gelatinous sheath has a higher density and no visible stratification. This layer glues the tightly packed capsules to one another and to the outer layers of the gelatinous sheath. The thin wall of the capsules is formed by a homogeneous and highly electron-dense material. Inside the capsules, the eggs or embryos were bathed in an electron-lucent aqueous medium. Bacteria and diatoms were the most abundant microorganisms on the surface of egg strings. Bacteria penetrate the gelatinous sheath and appear to be involved in the degradation of the upper strata, but were never found inside the egg capsules. Metagenomic analysis revealed a large taxonomic diversity of bacteria associated with egg masses of A. depilans . Although 15 phyla could be recognized, the families Flavobacteriaceae (Bacteroidota), Lentisphaeraceae (Lentisphaerota), and Rhodobacteraceae (Pseudomonadota) represented 67.9% ± 11.6% of the relative abundance in the microbiome of the egg string samples. The presence of genera capable of decomposing polysaccharides, such as Tenacibaculum and Cellulophaga , supports the idea that bacteria are responsible for the degradation of the gelatinous layers of the egg strings.

Microorganisms in the digestive tract regulate the metabolism of host cells as well as stimulate the immune system of the host. If the microbiota is in good balance, it will promote the good health of the host. In this study, using 16S rRNA sequencing, we analyzed the microbiota of three groups of shrimp: a group of normal shrimp (control group), shrimp that were killed by infection with the white spot syndrome virus (WSSV) (susceptible group), and shrimp that survived WSSV infection (resistant group). The results showed that although the alpha diversity of the microbiota was barely affected by the WSSV, the bacterial communities in the three groups had different prevalences. The resistant group harbored significantly more bacteria than both the other groups. Remarkably, the resistant group had the greatest prevalence of the phylum Bacterioidetes, the families Rhodobacteraceae and Flavobacteriaceae, and the genus Nautella, suggesting their potential as biomarkers for shrimp resistance to WSSV infection. In addition, analysis of functional diversity in bacterial communities showed that the abundance of bacterial metagenomes in two groups infected with WSSV was mostly linked to metabolism and cellular processes. The susceptible WSSV group exhibited a significant reduction in amino acid metabolism. This result suggested that metabolism was the principal factor affecting the alteration in the microbiota after WSSV infection. This overview of the gut microbiota of shrimp infected with the WSSV offers crucial insights for aquaculture management and simplifies the use of control strategies in the future.

Bioflocs are microbial aggregates primarily composed of heterotrophic bacteria that play essential ecological roles in maintaining animal health, gut microbiota, and water quality in biofloc aquaculture systems. Despite the global adoption of biofloc aquaculture for shrimp and fish cultivation, our understanding of biofloc microbiota-particularly the dominant bacterial members and their ecological functions-remains limited. In this study, we employed integrated metataxonomic and metagenomic approaches to demonstrate that the family Rhodobacteraceae of Alphaproteobacteria consistently dominates the biofloc microbiota and plays essential ecological roles. We first analyzed a comprehensive metataxonomic dataset consisting of 200 16S rRNA gene amplicons collected across three Asian countries: South Korea, China, and Vietnam. Taxonomic investigation identified Rhodobacteraceae as the dominant and consistent bacterial members across the datasets. The predominance of this taxon was further validated through metagenomics approaches, including read taxonomy and read recruitment analyses. To explore the ecological roles of Rhodobacteraceae, we applied genome-centric metagenomics, reconstructing 45 metagenome-assembled genomes. Functional annotation of these genomes revealed that dominant Rhodobacteraceae genera, such as Marivita, Ruegeria, Dinoroseobacter, and Aliiroseovarius, are involved in vital ecological processes, including complex carbohydrate degradation, aerobic denitrification, assimilatory nitrate reduction, ammonium assimilation, and sulfur oxidation. Overall, our study reveals that the common practice of carbohydrate addition in biofloc aquaculture systems fosters the growth of specific heterotrophic bacterial communities, particularly Rhodobacteraceae. These bacteria contribute to maintaining water quality by removing toxic nitrogen and sulfur compounds and enhance animal health by colonizing gut microbiota and exerting probiotic effects.

The Pacific oyster is the most widely cultured shellfish worldwide, but production has been affected by mortality events, including in hatcheries that supply the seed for growers. Several pathogens cause disease in oysters, but in many cases, mortality events cannot be attributed to a single agent and appear to be multifactorial, involving environmental variables and microbial interactions. As an organism's microbiome can provide resilience against pathogens and environmental stressors, we investigated the microbiomes in cohorts of freshly settled oyster spat, some of which experienced notable mortality. Deep sequencing of 16S rRNA gene fragments did not show a significant difference among the microbiomes of cohorts experiencing different mortality levels, but revealed a characteristic core microbiome comprising 74 taxa. Irrespective of mortality, the relative abundance of taxa in the core microbiomes changed significantly as the spat aged, yet remained distinct from the microbial community in the surrounding water. The core microbiome was dominated by bacteria in the families Rhodobacteraceae, Nitrosomonadaceae, Flavobacteriaceae, Pirellulaeceae, and Saprospiraceae. Within these families, 14 taxa designated as the "Hard-Core Microbiome" were indicative of changes in the core microbiome as the spat aged. The variability in diversity and richness of the core taxa decreased with age, implying niche occupation. As well, there was exchange of microbes with surrounding water during development of the core microbiome. The shift in the core microbiome demonstrates the dynamic nature of the microbiome as oyster spat age.IMPORTANCEThe Pacific oyster (Magallana gigas, also known as Crassostrea gigas) is the most widely cultivated shellfish and is important to the economy of many coastal communities. However, high mortality of spat during the first few days following metamorphosis can affect the seed supply to oyster growers. Here, we show that the microbiome composition of recently settled oyster spat experiencing low or high mortality was not significantly different. Instead, development of the core microbiome was associated with spat aging and was partially driven by dispersal through the water. These findings imply the importance of early-stage rearing conditions for spat microbiome development in aquaculture facilities. Furthermore, shellfish growers could gain information about the developmental state of the oyster spat microbiome by assessing key taxa. Additionally, the study provides a baseline microbiome for future hypothesis testing and potential probiotic applications on developing spat.

Facial aging is a complex process influenced by environmental factors, genetics, and lifestyle. The contribution of the skin microbiota to this process remains poorly understood. This two-sample Mendelian randomization (MR) study was performed using genome-wide genotype data from the UK Biobank and previously published studies on skin microbiota. The primary approach for MR analyses included inverse-variance weighting (IVW), MR-Egger regression, simple mode, weighted median, and weighted mode methods. Sensitivity analyses were performed to assess heterogeneity and pleiotropy, and reverse-direction MR analyses were performed to evaluate potential reverse causation. The MR analysis identified ten skin microbiotas with potential causal relationships with facial aging. Protective skin microbiotas included Genus Finegoldia, ASV011 [Staphylococcus (unc.)], ASV008 [Staphylococcus (unc.)], phylum Firmicutes, Family Rhodobacteraceae, and ASV021 [Micrococcus (unc.)], which were negatively associated with facial aging. Conversely, Order Pseudomonadales, Family Moraxellaceae, ASV039 [Acinetobacter (unc.)], and phylum Bacteroidetes were positively associated with facial aging, indicating a risk factor for accelerated aging. Sensitivity analyses confirmed the robustness of these findings, and reverse-direction MR analyses did not suggest any reverse causation. This study identified specific skin microbial that may influence facial aging and offered new insights into the rejuvenation strategies. This journal requires that authors assign a level of evidence to each submission to which Evidence-Based Medicine rankings are applicable. This excludes Review Articles, Book Reviews, and manuscripts that concern Basic Science, Animal Studies, Cadaver Studies, and Experimental Studies. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266 .

Microbial communities as indicators of marine ecosystem health: Insights from coastal sediments in the eastern Adriatic Sea

The Great Pacific Garbage Patch, a significant collection of plastic introduced by human activities, provides an ideal environment to study bacterial lifestyles on plastic substrates. We proposed that bacteria colonizing the floating plastic debris would develop strategies to deal with the ultraviolet-exposed substrate, such as the production of antioxidant pigments. We observed a variety of pigmentation in 67 strains that were directly cultivated from plastic pieces sampled from the Garbage Patch. The genomic analysis of four representative strains, each distinct in taxonomy, revealed multiple pathways for carotenoid production. These pathways include those that produce less common carotenoids and a cluster of photosynthetic genes. This cluster appears to originate from a potentially new species of the Rhodobacteraceae family. This represents the first report of an aerobic anoxygenic photoheterotrophic bacterium from plastic biofilms. Spectral analysis showed that the bacteria actively produce carotenoids, such as beta-carotene and beta-cryptoxanthin, and bacteriochlorophyll a. Furthermore, we discovered that the genetic ability to synthesize carotenoids is more common in plastic biofilms than in the surrounding water communities. Our findings suggest that plastic biofilms could be an overlooked source of bacteria-produced carotenoids, including rare forms. It also suggests that photoreactive molecules might play a crucial role in bacterial biofilm communities in surface water.

Prokaryotes dominate global oceans and shape biogeochemical cycles, yet most taxa remain uncultured and uncharacterized as of today. Here we present the characterization of 26 novel marine bacterial strains from a large isolate collection obtained from Blanes Bay (NW Mediterranean) microcosm experiments made in the four seasons. Morphological, cultural, biochemical, physiological, nutritional, genomic, and phylogenomic analyses were used to characterize and phylogenetically place the novel isolates. The strains represent 23 novel bacterial species and six novel genera: three novel species pertaining to class Alphaproteobacteria (families Rhodobacteraceae and Sphingomonadaceae), six novel species and three new genera from class Gammaproteobacteria (families Algiphilaceae, Salinispheraceae, and Alteromonadaceae), 13 novel species and three novel genera from class Bacteroidia (family Flavobacteriaceae), and one new species from class Rhodothermia (family Rubricoccaceae). The bacteria described here have potentially relevant roles in the cycles of carbon (e.g., carbon fixation or energy production via proteorhodopsin), nitrogen (e.g., denitrification or use of urea), sulfur (oxidation of sulfur compounds), phosphorus (acquisition and use of different forms of phosphorus and remodeling of membrane phospholipids), and hydrogen (oxidation of hydrogen to obtain energy). We mapped the genomes of the presented strains to the Tara Oceans metagenomes to reveal that these strains were globally distributed, with those of the family Flavobacteriaceae being the most widespread and abundant, while Rhodothermia being the rarest and most localized. While molecular-only approaches are also important, our study stresses the importance of culturing as a powerful tool to further understand the functioning of marine bacterial communities.

A Gram-stain-negative, aerobic, non-motile, catalase- and oxidase-positive, pale orange, rod-shaped strain EF6T, was isolated from a natural wetland reserve in Hebei province, China. The strain grew at 25-37°C (optimum, 30°C), pH 5-9 (optimum, pH 7), and in the presence of 1.0-4.0% (w/v) NaCl (optimum, 2%). A phylogenetic analysis based on 16S rRNA gene sequence revealed that strain EF6T belongs to the genus Paracoccus, and the closest members were Paracoccus shandongensis wg2T with 98.1% similarity, Paracoccus fontiphilus MVW-1T (97.9%), Paracoccus everestensis S8-55T (97.7%), Paracoccus subflavus GY0581T (97.6%), Paracoccus sediminis CMB17T (97.3%), Paracoccus caeni MJ17T (97.0%), and Paracoccus angustae E6T (97.0%). The genome size of strain EF6T was 4.88Mb, and the DNA G + C content was 65.3%. The digital DNA-DNA hybridization, average nucleotide identity, and average amino acid identity values between strain EF6T and the reference strains were all below the threshold limit for species delineation (< 32.8%, < 88.0%, and < 86.7%, respectively). The major fatty acids (≥ 5.0%) were summed feature 8 (86.3%, C18:1 ω6c and/or C18:1 ω7c) and C18:1 (5.0%) and the only isoprenoid quinone was Q-10. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, two unidentified glycolipids, five unidentified phospholipids, and an unidentified aminolipid. Strain EF6T displays notable resistance to benzoate and selenite, with higher tolerance levels (25 g/L for benzoate and 150 mM for selenite) compared to the closely related species. Genomic analysis identified six benzoate resistance genes (acdA, pcaF, fadA, pcaC, purB, and catA) and twenty selenite resistance and reduction-related genes (iscR, ssuB, ssuD, selA, selD and so on). Additionally, EF6T possesses unique genes (catA, ssuB, and ssuC) absent in the closely related species for benzoate and selenite resistance. Its robust resistance to benzoate and selenite, coupled with its genomic makeup, make EF6T a promising candidate for the remediation of both organic and inorganic pollutants. It is worth noting that the specific resistance phenotypes described above were not reported in other novel species in Paracoccus. Based on the results of biochemical, physiological, phylogenetic, and chemotaxonomic analyses, combined with comparisons of the 16S rRNA gene sequence and the whole genome sequence, strain EF6T is considered to represent a novel species of the genus Paracoccus within the family Rhodobacteraceae, for which the name Paracoccus benzoatiresistens sp. nov. is proposed. The type strain is EF6T (= GDMCC 1.3400T = JCM 35642T = MCCC 1K08702T).

Plant microbiomes are known to serve several important functions for their host, and it is therefore important to understand their composition as well as the factors that may influence these microbial communities. The microbiome of Thalassia testudinum has only recently been explored, and studies to-date have primarily focused on characterizing the microbiome of plants in a single region. Here, we present the first characterization of the composition of the microbial communities of T. testudinum across a wide geographical range spanning three distinct regions with varying physicochemical conditions. We collected samples of leaves, roots, sediment, and water from six sites throughout the Atlantic Ocean, Caribbean Sea, and the Gulf of Mexico. We then analyzed these samples using 16S rRNA amplicon sequencing. We found that site and region can influence the microbial communities of T. testudinum, while maintaining a plant-associated core microbiome. A comprehensive comparison of available microbial community data from T. testudinum studies determined a core microbiome composed of 14 ASVs that consisted mostly of the family Rhodobacteraceae. The most abundant genera in the microbial communities included organisms with possible plant-beneficial functions, like plant-growth promoting taxa, disease suppressing taxa, and nitrogen fixers.