The bacterial community from estuarine sediment undertakes the bioremediation and energy transformation of anthropogenic pollutants especially polycyclic aromatic hydrocarbons (PAHs). However, information and studies on bacterial synergism and related metabolic profiles under the stress of PAHs are limited. In this study, sediments from estuarine were collected and co-incubated with a classical PAH, pyrene. The results showed that Alpha- and Gammaproteobacteria became abundant at the late domesticating phase with the dominant genus of ZD0117, the uncultivated bacteria affiliated into Gammaproteobacteria. Functional gene analysis based on metagenomic sequencing showed that quantitatively changes of genes directly related to the degradation of aromatic hydrocarbon coordinated with genes involved into various metabolic pathways such as acylglycerol degradation, nitrogen fixation, sulfate transport system, Arnon-Buchanan cycle, and Calvin cycle (P < 0.01 and |ρ| > 0.8). Fifty-six metagenome-assembled genomes (MAGs) were reconstructed, which were primarily composed by Alpha- and Gammaproteobacteria. Bacteria belonging to the phylum Proteobacteria were found to be abundant in MAGs and contained genes encoding for dehydrogenase, which are key enzymes for pyrene degradation. In addition, genomes of uncultivated bacteria were successfully reconstructed and were proven to carry genes of synergistically metabolizing pyrene. Based on analysis of typical MAGs, the metabolic pathways involved in syntrophic associations of a pyrene-degrading consortium were reconstructed. The results in this study could make us fully understand the metabolic patterns of pyrene-degrading consortium from the estuarine sediment and widen the scope of functional bacteria.

Sustainable biofuels, which are widely considered as an attractive alternative to fossil fuels, can be generated by utilizing various biomass from the environment. Marine biomass, such as red algal biomass, is regarded as one potential renewable substrate source for biofuels conversion due to its abundance of fermentable sugars (e.g., galactose). Previous studies focused on the enhancement of biofuels production from different Clostridium species; however, there has been limited investigation into their metabolic pathways, especially on the conversion of biofuels from galactose, via whole genomic comparison and evolutionary analysis. Two galactose-utilizing Clostridial strains were examined and identified as Clostridium acetobutylicum strain WA and C. beijerinckii strain WB. Via the genomic sequencing of both strains, the comparison of the whole genome together with the relevant protein prediction of 33 other Clostridium species was established to reveal a clear genome profile based upon various genomic features. Among them, five representative strains, including C. beijerinckii NCIMB14988, C. diolis DSM 15410, C. pasteurianum BC1, strain WA and WB, were further discussed to demonstrate the main differences among their respective metabolic pathways, especially in their carbohydrate metabolism. The metabolic pathways involved in the generation of biofuels and other potential products (e.g., riboflavin) were also reconstructed based on the utilization of marine biomass. Finally, a batch fermentation process was performed to verify the fermentative products from strains WA and WB using 60 g/L of galactose, which is the main hydrolysate from algal biomass. It was observed that strain WA and WB could produce up to 16.98 and 12.47 g/L of biobutanol, together with 21,560 and 10,140 mL/L biohydrogen, respectively. The determination of the production of various biofuels by both strains WA and WB and their genomic comparisons with other typical Clostridium species on the analysis of various metabolic pathways was presented. Through the identification of their metabolic pathways, which are involved in the conversion of galactose into various potential products, such as biobutanol, the obtained results extend the current insight into the potential capability of utilizing marine red algal biomass and provide a systematic investigation into the relationship between this genus and the generation of sustainable bioenergy.

An aerobic, Gram-stain-negative, rod-shaped, non-motile bacterium capable of degrading the polycyclic aromatic hydrocarbon pyrene was isolated from sediment of Pearl River and designated PrR001. 16S rRNA gene sequence analysis revealed that this strain was affiliated within the genus Defluviimonas in the family Rhodobacteraceae of the class Alphaproteobacteria and showed great similarity with the type strain Defluviimonas indica 20V17(T) (96.3 % similarity). The DNA G+C content of strain PrR001(T) was 68.3 mol%. The major cellular fatty acids comprised summed feature 8 (C(18:1)w7c/C(18:1)w6c), C-19:0 cyclo w8c, C-18:0 30H, and C-18:0. The sole respiratory lipoquinone was ubiquinone-10. The main polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminolipid, an unidentified aminophospholipid and three unidentified phospholipids. Based on physiological, chemotaxonomic and phylogenetic analysis, strain PrR001(T) is suggested as a novel species in the genus Defluviimonas, for which the name Defluviimonas pyrenivorans sp. nov. is proposed. The type strain of Defluviimonas pyrenivorans is PrR001(T) (=CICC 24263(T)=KCTC 62192(T)).

The phylogenetic diversity of bacterial communities in response to environmental disturbances such as organic pollution has been well studied, but little is known about the way in which organic contaminants influence the acclimation of functional bacteria. In the present study, tolerance assays for bacterial communities from the sediment in the Pearl River Estuary were conducted with the isolation of functional bacteria using pyrene and different estrogens as environmental stressors. Molecular ecological networks and phylogenetic trees were constructed using both 16S rRNA gene sequences of cultured bacterial strains and 16S rRNA gene based pyrosequencing data to illustrate the successions of bacterial communities and their acclimations to the different organic compounds. One hundred and eleven bacterial strains exhibiting degradation and endurance capabilities in response to the pyrene estrogen-induced stress were successfully isolated and were mainly affiliated with three orders, Pseudomonadales, Vibrionales, and Rhodobacterales. Molecular ecological networks and phylogenetic trees showed various adaptive abilities of bacteria to the different organic compounds. For instance, some bacterial OTUs could be found only in particular organic compound-treated groups while some other OTUs could tolerate stresses from different organic compounds. Furthermore, the results indicated that some new phylotypes were emerged under stresses of different organic pollutions and these new phylotypes could adapt to the contaminated environments and contribute significantly to the microbial community shifts. Overall, this study demonstrated a crucial role of the community succession and the acclimation of functional bacteria in the adaptive responses to various environmental disturbances.

A Gram-negative, aerobic, rod-shaped, non-motile by gliding bacterium was isolated from the estuarine sediment of the Pearl River in PR China and designated as strain q18^T. Colonies were circular, smooth and yellow on marine agar after 48 h cultivation. Salinity, temperature and pH for optimal growth were 5 % (NaCl), 30 °C and 7, respectively. The 16S rRNA gene sequence of the strain q18^T showed the highest similarity of 97.3 % to the type strain of Aequorivita echinoideorum CC-CZW007^T. 16S rRNA gene-based phylogenetic analysis indicated that strain q18^T grouped into the genus Aequorivita in the family Flavobacteriaceae of the phylum Bacteroidetes , and was distinct from all known species in the genus. Menaquinone (MK-6) was the main respiratory quinone detected in strain q18^T. The major fatty acids were iso-C_15 : 0 and iso-C_17 : 0 3-OH. The polar lipids of strain q18^T mainly comprised phosphatidylethanolamine, two unidentified aminolipids, two unidentified phospholipids and one unidentified polar lipid. The G+C content of the genome was ~42.8 mol%. The draft genome size of strain q18^T was 3.3 Mbp. The average nucleotide identity values were around 79.0 % between strain q18^T and reference Aequorivita strains. Based on the polyphasic analysis, strain q18^T was confirmed to represent a novel species of the genus Aequorivita , for which the name Aequorivita lutea sp. nov., is proposed. The type strain is q18^T (=CICC 24821^T=KCTC 72764 ^T). Further, based on the results of phylogenetic, chemotaxonomic and phenotypic analyses, two species previously classified into the genus Vitellibacter , Vitellibacter todarodis Kim et al. 2018 and Vitellibacter aquimaris Thevarajoo et al. 2016, are transferred to the genus Aequorivita as Aequorivita todarodis comb. nov. and Aequorivita aquimaris comb. nov. respectively.