Isolation, molecular identification, and genomic analysis of Mangrovibacter phragmitis strain ASIOC01 from activated sludge harboring the bioremediation prowess of glycerol and organic pollutants in high-salinity

The physiological and genotypic characteristics of Mangrovibacter (MGB) remain largely unexplored, including their distribution and abundance within ecosystems. M. phragmitis (MPH) ASIOC01 was successfully isolated from activated sludge (AS), which was pre-enriched by adding 1,3-dichloro-2-propanol and 3-chloro-1,2-propanediol as carbon sources. The new isolate, MPH ASIOC01, exhibited resilience in a medium containing sodium chloride concentration up to 11% (with optimal growth observed at 3%) and effectively utilizing glycerol as their sole carbon source. However, species delimitation of MGBs remains challenging due to high 16S rRNA sequence similarity (greater than 99% ANI) among different MGBs. In contrast, among the housekeeping gene discrepancies, the tryptophan synthase beta chain gene can serve as a robust marker for fast species delimitation among MGBs. Furthermore, the complete genome of MPH ASIOC01 was fully sequenced and circlized as a single contig using the PacBio HiFi sequencing method. Comparative genomics revealed genes potentially associated with various phenotypic features of MGBs, such as nitrogen-fixing, phosphate-solubilizing, cellulose-digesting, Cr-reducing, and salt tolerance. Computational analysis suggested that MPH ASIOC01 may have undergone horizontal gene transfer events, possibly contributing unique traits such as antibiotic resistance. Finally, our findings also disclosed that the introduction of MPH ASIOC01 into AS can assist in the remediation of wastewater chemical oxygen demand, which was evaluated using gas chromatograph-mass spectrometry. To the best of our knowledge, this study offers the most comprehensive understanding of the phenotypic and genotypic features of MGBs to date.

Contribution of Aerobic Cellulolytic Gut Bacteria to Cellulose Digestion in Fifteen Coastal Grapsoid Crabs Underpins Potential for Mineralization of Mangrove Production

Grapsoid crabs (Decapoda: Grapsoidea) inhabiting along the land-sea transition provided various amounts and quality of vascular plant carbon (e.g., fresh mangrove leaf, leaf litter, and mangrove-derived organic carbon) and perform differing levels of herbivory. Other than endogenous cellulase, symbiotic cellulolytic bacteria could also contribute to the crabs' vascular plant carbon assimilation and mineralization. In this study, we isolated culturable cellulolytic bacteria from three gut regions (i.e., stomach, midgut, and hindgut) of 15 species of grapsoid crabs that inhabit in various coastal habitats (i.e., land margin, mangrove forest, tidal flat, and subtidal area). Bacillus, which was isolated from 11 out of the 15 grapsoid crabs, was the most common genus of culturable prominently cellulolytic bacteria among the target species. Seventy to ninety nine percent of culturable cellulolytic bacteria were removed, and the endoglucanase activity of five species was significantly reduced by 14.4-27.7% after antibiotic treatment. These results suggest that cellulolytic bacteria play a role in assisting mangrove carbon utilization in coastal grapsoid crabs, especially those inhabiting mangrove, mudflat, and subtidal areas. The significantly higher abundance of cellulolytic bacteria and the generally higher hydrolytic capacity of the bacteria in mangrove crab species suggest that they receive more contribution from symbionts for mangrove carbon utilization, while semi-terrestrial crabs seem to depend little on symbiotic cellulase due to the lower abundances.

Tenebrionibacter intestinalis gen. nov., sp. nov., a member of a novel genus of the family Enterobacteriaceae, isolated from the gut of the plastic-eating mealworm Tenebrio molitor L

A Gram-negative, white-pigmented, motile and rod-shaped strain, BIT-L3T, was isolated from the gut of plastic-eating mealworm Tenebrio molitor L. Its taxonomic position was determined by using a polyphasic approach. A preliminary analysis based on the 16S rRNA gene sequence (1445 bp) revealed that this strain was closely related to the members within the family Enterobacteriaceae . Phylogenetic trees based on the concatenated partial sequences of seven housekeeping genes (atpD, gyrB, infB, rpoB, pyrG, fusA, leuS) and genome sequences further showed that strain BIT-L3T constituted a separate lineage within the family Enterobacteriaceae. In silico DNA–DNA hybridization values and average nucleotide identity values between strain BIT-L3T and its closest related species within the family Enterobacteriaceae were less than 21.8 and 76.7 %, respectively. The major fatty acids (>5 %) of strain BIT-L3T were C16 : 0, C14 : 0, C17 : 0 cyclo, summed feature 8 (comprising C18 : 1 ω7c and/or C18 : 1 ω6c), summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω6c and/or iso-C15 : 0 2-OH) and summed feature 2 (comprising iso-C16 : 1 I/C14 : 0 3-OH and/or C12 : 0 aldehyde and/or an unknown fatty acid of equivalent chain length 10.9525). Its genomic DNA G+C content was 53.7 mol%. Based on the results of phylogenetic, physiological and biochemical analyses, strain BIT-L3T is considered to represent a novel species of a novel genus within the family Enterobacteriaceae , for which the name Tenebrionibacter intestinalis gen. nov., sp. nov. is proposed. The type strain is BIT-L3T (=CCTCC AB 2020371T=LMG 32222T=TBRC 14825T).

Diverse key nitrogen cycling genes nifH, nirS and nosZ associated with Pichavaram mangrove rhizospheres as revealed by culture-dependent and culture-independent analyses

Mangroves are highly productive unique ecosystems harboring diverse unexplored microbial communities that play crucial roles in nutrient cycling as well as in maintaining ecosystem services. The mangrove-associated microbial communities transform the dead vegetation into nutrient sources of nitrogen, phosphorus, potash, etc. To understand the genetic and functional diversity of the bacterial communities involved in nitrogen cycling of this ecosystem, this study explored the diversity and distribution of both the nitrogen fixers and denitrifiers associated with the rhizospheres of Avicennia marina, Rhizophora mucronata, Suaeda maritima, and Salicornia brachiata of the Pichavaram mangroves. A combination of both culturable and unculturable (PCR-DGGE) approaches was adopted to explore the bacterial communities involved in nitrogen fixation by targeting the nifH genes, and the denitrifiers were explored by targeting the nirS and nosZ genes. Across the rhizospheres, Gammaproteobacteria was found to be predominant representing both nitrogen fixers and denitrifiers as revealed by culturable and unculturable analyses. Sequence analysis of soil nifH, nirS and nosZ genes clustered to unculturable, with few groups clustering with culturable groups, viz., Pseudomonas sp. and Halomonas sp. A total of 16 different culturable genera were isolated and characterized in this study. Other phyla like Firmicutes and Actinobacteria were also observed. The PCR-DGGE analysis also revealed the presence of 29 novel nifH sequences that were not reported earlier. Thus, the mangrove ecosystems serve as potential source for identifying unexplored novel microbial communities that contribute to nutrient cycling.

The Changing Face of the Family Enterobacteriaceae (Order: "Enterobacterales"): New Members, Taxonomic Issues, Geographic Expansion, and New Diseases and Disease Syndromes

The family Enterobacteriaceae has undergone significant morphogenetic changes in its more than 85-year history, particularly during the past 2 decades (2000 to 2020). The development and introduction of new and novel molecular methods coupled with innovative laboratory techniques have led to many advances. We now know that the global range of enterobacteria is much more expansive than previously recognized, as they play important roles in the environment in vegetative processes and through widespread environmental distribution through insect vectors. In humans, many new species have been described, some associated with specific disease processes. Some established species are now observed in new infectious disease settings and syndromes. The results of molecular taxonomic and phylogenetics studies suggest that the current family Enterobacteriaceae should possibly be divided into seven or more separate families. The logarithmic explosion in the number of enterobacterial species described brings into question the relevancy, need, and mechanisms to potentially identify these taxa. This review covers the progression, transformation, and morphogenesis of the family from the seminal Centers for Disease Control and Prevention publication (J. J. Farmer III, B. R. Davis, F. W. Hickman-Brenner, A. McWhorter, et al., J Clin Microbiol 21:46-76, 1985, https://doi.org/10.1128/JCM.21.1.46-76.1985) to the present.

Free-Living Enterobacterium Pragia fontium 24613: Complete Genome Sequence and Metabolic Profiling

Pragia fontium is one of the few species that belongs to the group of atypical hydrogen sulfide-producing enterobacteria. Unlike other members of this closely related group, P. fontium is not associated with any known host and has been reported as a free-living bacterium. Whole genome sequencing and metabolic fingerprinting confirmed the phylogenetic position of P. fontium inside the group of atypical H₂S producers. Genomic data have revealed that P. fontium 24613 has limited pathogenic potential, although there are signs of genome decay. Although the lack of specific virulence factors and no association with a host species suggest a free-living style, the signs of genome decay suggest a process of adaptation to an as-yet-unknown host.

The draft genome sequence of Mangrovibacter sp. strain MP23, an endophyte isolated from the roots of Phragmites karka

Till date, only one draft genome has been reported within the genus Mangrovibacter. Here, we report the second draft genome shotgun sequence of a Mangrovibacter sp. strain MP23 that was isolated from the roots of Phargmites karka (P. karka), an invasive weed growing in the Chilika Lagoon, Odisha, India. Strain MP23 is a facultative anaerobic, nitrogen-fixing endophytic bacteria that grows optimally at 37 °C, 7.0 pH, and 1% NaCl concentration. The draft genome sequence of strain MP23 contains 4,947,475 bp with an estimated G + C content of 49.9% and total 4392 protein coding genes. The genome sequence has provided information on putative genes that code for proteins involved in oxidative stress, uptake of nutrients, and nitrogen fixation that might offer niche specific ecological fitness and explain the invasive success of P. karka in Chilika Lagoon. The draft genome sequence and annotation have been deposited at DDBJ/EMBL/GenBank under the accession number LYRP00000000.

Mangrovibacter yixingensis sp. nov., isolated from farmland soil

A Gram-staining-negative, facultatively anaerobic, rod-shaped, nitrogen-fixing bacterial strain, designated TULL-AT, was isolated from a farmland soil sample in Yixing, China. The optimal conditions for growth were 30 °C, pH 7.0-8.0 and 0% (w/v) NaCl. Q8 was the dominant respiratory quinone and the major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and aminophospholipid. Phylogenetic analysis of 16S rRNA gene sequences showed that strain TULL-AT was most closely related to Mangrovibacter plantisponsor MSSRF40T (99.6%), followed by Salmonella enterica subsp. diarizonae DSM 14847T (96.8%) and Cronobacter condimenti 1330T (96.8 %). Sequence analysis of the genes rpoB, gyrB and hsp60 revealed that those of strain TULL-AT also exhibit high sequence similarity with those of the species M. plantisponsor MSSRF40T (95.5, 94.1 and 93.4%). The genomic DNA G+C content was 52 mol%. The major fatty acids of strain TULL-AT were C16 : 0, C16 : 1ω7c and/or C16 : 1ω6c, C18 : 1ω7c /C18 : 1ω6c, C14 : 0, C14 : 0 3-OH/iso-C16 : 1 I and iso-C17 : 1 I and/or anteiso-C17 : 1 B. Strain TULL-AT showed low DNA-DNA relatedness with M. plantisponsor MSSRF40T (35.10 ± 1.41%). Based on the multiple genotypic and phenotypic data, strain TULL-AT is considered to represent a novel species of the genus Mangrovibacter, for which the name Mangrovibacter yixingensis sp. nov. is proposed. The type strain is TULL-AT ( = ACCC 19709T = KCTC 42181T).

First draft genome sequence of a member of the genus mangrovibacter, isolated from an aquaculture farm in India

Mangrovibacter sp. MFB070, a Gram-negative, facultatively anaerobic, nitrogen-fixing bacterium, was isolated from an aquaculture farm in Cochin, India. Here, we report the first draft genome sequence of a member of the genus Mangrovibacter, which may help us to elucidate the evolutionary status of this genus. The draft genome sequence of the Mangrovibacter sp. consists of 5,361,682 bp, encoding 4,971 predicted coding sequences in 57 contigs.

Whole genome sequencing and analysis of plant growth promoting bacteria isolated from the rhizosphere of plantation crops coconut, cocoa and arecanut

Coconut, cocoa and arecanut are commercial plantation crops that play a vital role in the Indian economy while sustaining the livelihood of more than 10 million Indians. According to 2012 Food and Agricultural organization's report, India is the third largest producer of coconut and it dominates the production of arecanut worldwide. In this study, three Plant Growth Promoting Rhizobacteria (PGPR) from coconut (CPCRI-1), cocoa (CPCRI-2) and arecanut (CPCRI-3) characterized for the PGP activities have been sequenced. The draft genome sizes were 4.7 Mb (56% GC), 5.9 Mb (63.6% GC) and 5.1 Mb (54.8% GB) for CPCRI-1, CPCRI-2, CPCRI-3, respectively. These genomes encoded 4056 (CPCRI-1), 4637 (CPCRI-2) and 4286 (CPCRI-3) protein-coding genes. Phylogenetic analysis revealed that both CPCRI-1 and CPCRI-3 belonged to Enterobacteriaceae family, while, CPCRI-2 was a Pseudomonadaceae family member. Functional annotation of the genes predicted that all three bacteria encoded genes needed for mineral phosphate solubilization, siderophores, acetoin, butanediol, 1-aminocyclopropane-1-carboxylate (ACC) deaminase, chitinase, phenazine, 4-hydroxybenzoate, trehalose and quorum sensing molecules supportive of the plant growth promoting traits observed in the course of their isolation and characterization. Additionally, in all the three CPCRI PGPRs, we identified genes involved in synthesis of hydrogen sulfide (H2S), which recently has been proposed to aid plant growth. The PGPRs also carried genes for central carbohydrate metabolism indicating that the bacteria can efficiently utilize the root exudates and other organic materials as energy source. Genes for production of peroxidases, catalases and superoxide dismutases that confer resistance to oxidative stresses in plants were identified. Besides these, genes for heat shock tolerance, cold shock tolerance and glycine-betaine production that enable bacteria to survive abiotic stress were also identified.

Rosenbergiella nectarea gen. nov., sp. nov., in the family Enterobacteriaceae, isolated from floral nectar

Gram-negative, rod-shaped, oxidase-negative, facultatively anaerobic, yellow-orange-pigmented and motile bacterial strains, designated 8N4(T), 9N2 and 10N3, were isolated from flower nectar of Amygdalus communis (almond) and Citrus paradisi (grapefruit). The 16S rRNA gene sequences of the strains shared highest sequence similarity of 97.0 % with that of Phaseolibacter flectens ATCC 12775(T) and lower similarity with sequences from other type strains of genera of the Enterobacteriaceae. A polyphasic approach that included determination of phenotypic properties and phylogenetic analysis based on 16S rRNA, gyrB, rpoB and atpD gene sequences supported the classification of strains 8N4(T), 9N2 and 10N3 within a novel species in a novel genus in the family Enterobacteriaceae. Strain 8N4(T), and the reference strains of the novel species, grew at 4-35 °C (optimum, 28-30 °C), with 0-5.0 % NaCl (optimum, 3 % NaCl) and with 0-60 % sucrose (optimum, 10-25 % sucrose). Their major cellular fatty acids were C16 : 0, C17 : 0 cyclo, C18 : 1ω7c and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The DNA G+C content of strain 8N4(T) was 46.8 mol%. On the basis of phenotypic properties and phylogenetic distinctiveness, the floral nectar isolates are classified within a novel species in a new genus in the family Enterobacteriaceae, for which the name Rosenbergiella nectarea gen. nov., sp. nov. is proposed. The type strain of Rosenbergiella nectarea is 8N4(T) ( = LMG 26121(T) = DSM 24150(T)).

Budvicia diplopodorum sp. nov. and emended description of the genus Budvicia

A Gram-negative, rod-shaped, weakly motile, non-spore-forming bacterium (D9T) was isolated from the gut of Cylindroiulus fulviceps (Diplopoda) on 1/3-strength nutrient agar plates. On the basis of 16S rRNA gene sequence similarity, strain D9T was shown to be phylogenetically closely related to the type strain of Budvicia aquatica , the sole species of the genus Budvicia , family Enterobacteriaceae . The similarity of the 16S rRNA gene sequences of strain D9T and B. aquatica DSM 5075T was 98.4 %. Other strains that showed high pairwise similarities with the isolate belonged to the genus Yersinia : Y. frederiksenii ATCC 33641T (96.8 % 16S rRNA gene sequence similarity), Y. massiliensis CCUG 53443T (96.8 %), Y. pestis NCTC 5923T (96.8 %), Y. pseudotuberculosis ATCC 29833T (96.8 %), Y. similis CCUG 52882T (96.7 %) and Y. ruckeri ATCC 29473T (96.5 % ). The similarities of sequences of the housekeeping genes rpoB, hsp60 and gyrB between strain D9T and B. aquatica DSM 5075T and other members of the Enterobacteriaceae were less than 94 %. Phylogenetic trees based on all four gene sequences unequivocally grouped the isolate with the type strain of B. aquatica and separately from the genus Yersinia . Cells contained the quinones Q-8, Q-7 and MK-8. The major polar lipids were phosphatidylglycerol and phosphatidylethanolamine. The G+C content of the DNA (48.3 mol%) and the whole-cell fatty acid composition of strain D9T (C14 : 0, C16 : 1ω7c, C16 : 0, cyclo-C17 : 0 and C18 : 1ω7c as major components) were typical for members of the Enterobacteriaceae . DNA–DNA hybridization of strain D9T with B. aquatica DSM 5075T resulted in a relatedness of 30.4 %, indicating that the isolate did not belong to B. aquatica . Physiological tests allowed the phenotypic differentiation of strain D9T from B. aquatica DSM 5075T as well as from members of the genus Yersinia . From these results, it is concluded that strain D9T represents a novel species, for which the name Budvicia diplopodorum sp. nov. is proposed (type strain D9T  = DSM 21983T  = CCM 7845T). The description of the genus Budvicia is emended.

Transfer of Pseudomonas flectens Johnson 1956 to Phaseolibacter gen. nov., in the family Enterobacteriaceae , as Phaseolibacter flectens gen. nov., comb. nov

Pseudomonas flectens Johnson 1956, a plant-pathogenic bacterium on the pods of the French bean, is no longer considered to be a member of the genus Pseudomonas sensu stricto. A polyphasic approach that included examination of phenotypic properties and phylogenetic analyses based on 16S rRNA, rpoB and atpD gene sequences supported the transfer of Pseudomonas flectens Johnson 1956 to a new genus in the family Enterobacteriaceae as Phaseolibacter flectens gen. nov., comb. nov. Two strains of Phaseolibacter flectens were studied (ATCC 12775T and LMG 2186); the strains shared 99.8 % sequence similarity in their 16S rRNA genes and the housekeeping gene sequences were identical. Strains of Phaseolibacter flectens shared 96.6 % or less 16S rRNA gene sequence similarity with members of different genera in the family Enterobacteriaceae and only 84.7 % sequence similarity with Pseudomonas aeruginosa LMG 1242T, demonstrating that they are not related to the genus Pseudomonas . As Phaseolibacter flectens formed an independent phyletic lineage in all of the phylogenetic analyses, it could not be affiliated to any of the recognized genera within the family Enterobacteriaceae and therefore was assigned to a new genus. Cells were Gram-negative, straight rods, motile by means of one or two polar flagella, fermentative, facultative anaerobes, oxidase-negative and catalase-positive. Growth occurred in the presence of 0–60 % sucrose. The DNA G+C content of the type strain was 44.3 mol%. On the basis of phenotypic properties and phylogenetic distinctiveness, Pseudomonas flectens Johnson 1956 is transferred to the novel genus Phaseolibacter gen. nov. as Phaseolibacter flectens gen. nov., comb. nov. The type strain of Phaseolibacter flectens is ATCC 12775T  = CFBP 3281T  = ICMP 745T  = LMG 2187T  = NCPPB 539T.

Vibrio plantisponsor sp. nov., a diazotrophic bacterium isolated from a mangrove associated wild rice (Porteresia coarctata Tateoka)

Two Gram negative, facultatively anaerobic, halophilic, motile, slightly curved rod-shaped bacterial strains MSSRF60(T) and MSSRF64 were isolated from the roots of a mangrove-associated wild rice collected in the Pichavaram mangroves, India. These strains possess the key functional nitrogenase gene nifH. Phylogenetic analysis based on the 16S rRNA, recA, gapA, mreB, gyrB and pyrH, gene sequences revealed that strains MSSRF60(T) and MSSRF64 belong to the genus Vibrio, and had the highest sequence similarity with the type strains of Vibrio diazotrophicus LMG 7893(T) (99.7, 94.8, 98.5, 97.9, 94.0 and 90.7%, respectively), Vibrio areninigrae J74(T) (98.2, 87.5, 91.5, 88.9, 86.5 and 84.6% respectively) and Vibrio hispanicus LMG 13240(T) (97.8, 87.1, 91.7, 89.8, 84.1 and 81.9%, respectively). The fatty acid composition too confirmed the affiliation of strains MSSRF60(T) and MSSRF64 to the genus Vibrio. These strains can be differentiated from the most closely related Vibrio species by several phenotypic traits. The DNA G+C content of strain MSSRF60(T) was 41.8mol%. Based on phenotypic, chemotaxonomic, genotypic (multilocus sequence analysis using five genes and genomic fingerprinting using BOX-PCR) and DNA-DNA hybridization analyses, strains MSSRF60(T) and MSSRF64 represent a novel species of the genus Vibrio, for which the name Vibrio plantipsonsor sp. nov. is proposed. The type strain is MSSRF60(T) (=DSM 21026(T)=LMG 24470(T)=CAIM 1392(T)).