Bacterial nanocellulose production from naphthalene

Impact of Arsenic and PAHs compound contamination on microorganisms in coking sites: from a community to individual perspective

Arsenic (As) and polycyclic aromatic hydrocarbons (PAHs) are highly toxic, carcinogenic and teratogenic, and are commonly found in soils of industrial sites such as coking plants. They exert environmental stresses on soil microorganisms, but their compounding effects have not been systematically studied. Exploring the effects of compound contamination on microbial communities, species and genes is important for revealing the ecological damage caused by compound contamination and offering scientific insights into soil remediation strategies. In this study, we selected soil samples from 0-100 cm depth of a coking site with As, PAHs and compound contamination. We investigated the compound effects of As and PAHs on microbial communities by combining high-throughput sequencing, metagenomic sequencing and genome assembly. Compared with single contamination, compound contamination reduced the microbial community diversity by 10.68%∼12.07% and reduced the community richness by 8.39%∼18.61%. The compound contamination decreased 32.41%∼46.02% of microbial PAHs metabolic gene abundance, 11.36%∼19.25% of cell membrane transport gene abundance and 12.62%∼57.77% of cell motility gene abundance. Xanthobacteraceae, the biomarker for compound contaminated soils, harbors arsenic reduction genes and PAHs degradation pathways of naphthalene, benzo[a]pyrene, fluorene, anthracene, and phenanthrene. Its broad metabolic capabilities, encompassing sulfur metabolism and quorum sensing, facilitate the acquisition of energy and nutrients, thereby conferring ecological niche advantages in compound contaminated environments. This study underscores the significant impacts of As and PAHs on the composition and function of microbial communities, thereby enriching our understanding of their combined effects and providing insights for the remediation of compound contaminated sites.

Cultivation and characterization of functional-yet-uncultivable phenanthrene degraders by stable-isotope-probing and metagenomic-binning directed cultivation (SIP-MDC)

High-throughput identification and cultivation of functional-yet-uncultivable microorganisms is a fundamental goal in environmental microbiology. It remains as a critical challenge due to the lack of routine and effective approaches. Here, we firstly proposed an approach of stable-isotope-probing and metagenomic-binning directed cultivation (SIP-MDC) to isolate and characterize the active phenanthrene degraders from petroleum-contaminated soils. From SIP and metagenome, we assembled 13 high-quality metagenomic bins from 13C-DNA, and successfully obtained the genome of an active PHE degrader Achromobacter (genome-MB) from 13C-DNA metagenomes, which was confirmed by gyrB gene comparison and average nucleotide/amino identity (ANI/AAI), as well as the quantification of PAH dioxygenase and antibiotic resistance genes. Thereinto, we modified the traditional cultivation medium with antibiotics and specific growth factors (e.g., vitamins and metals), and separated an active phenanthrene degrader Achromobacter sp. LJB-25 via directed isolation. Strain LJB-25 could degrade phenanthrene and its identity was confirmed by ANI/AAI values between its genome and genome-MB (>99 %). Our results hinted at the feasibility of SIP-MDC to identify, isolate and cultivate functional-yet-uncultivable microorganisms (active phenanthrene degraders) from their natural habitats. Our findings developed a state-of-the-art SIP-MDC approach, expanded our knowledge on phenanthrene biodegradation mechanisms, and proposed a strategy to mine functional-yet-uncultivable microorganisms.

Ancylobacter radicis sp. nov., a novel aerobic methylotrophic bacteria associated with plants

The two novel bacterial strains, designated as VT^T and ML, were isolated from roots of cinquefoil (Potentilla sp.) and leaves of meadow-grass (Poa sp.) on the flooded bank of lake, respectively. These isolates were Gram-negative, non-spore-forming, non-motile, rod-shaped cells, utilized methanol, methylamine, and polycarbon compounds as carbon and energy sources. In the whole-cell fatty acid pattern of strains prevailed C_18:1ω7c and C_19:0cyc. Based on the phylogenetic analysis of 16S rRNA gene sequences, strains VT^T and ML were closely related to the representatives of the genus Ancylobacter (98.3-98.5%). The assembled genome of strain VT^T has a total length of 4.22 Mbp, and a G + C content is 67.3%. The average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA-DNA hybridization (dDDH) values between strain VT^T and closely related type strains of genus Ancylobacter were 78.0-80.6%, 73.8-78.3% and 22.1-24.0%, respectively, that clearly lower than proposed thresholds for species. On the basis of the phylogenetic, phenotypic, and chemotaxonomic analysis, isolates VT^T and ML represent a novel species of the genus Ancylobacter, for which the name Ancylobacter radicis sp. nov. is proposed. The type strain is VT^T (= VKM B-3255^T = CCUG 72400^T). In addition, novel strains were able to dissolve insoluble phosphates, to produce siderophores and plant hormones (auxin biosynthesis). According to genome analysis genes involved in the biosynthesis of siderophores, polyhydroxybutyrate, exopolysaccharides and phosphorus metabolism, as well as the genes involved in the assimilation of C₁-compounds (natural products of plant metabolism) were found in the genome of type strain VT^T.

Potato thermoplastic starch nanocomposite films reinforced with nanocellulose

Potato is a widely available feedstock with biocompatibility and biodegradability properties, making it a strong candidate for producing thermoplastic starch. The application of thermoplastic starch to replace petroleum-based plastic as a sustainable and environmentally friendly approach led to its further improvement through various techniques such as modification and filler reinforcement. Numerous studies have been done addressing the properties enhancement of potato thermoplastic starch through filler reinforcement including nanocellulose. This review focus on the recent and future potential of potato-based starch as one of the feedstocks for producing potato thermoplastic starch composites reinforced with nanocellulose.

Ancylobacter moscoviensis sp. nov., novel facultatively methylotrophic bacteria from activated sludge and the reclassification of Starkeya novella (Starkey 1934) Kelly et al. 2000 as Ancylobacter novellus comb. nov., Starkeya koreensis Im et al. 2006 as Ancylobacter koreensis comb.nov., Angulomicrobium tetraedrale Vasil'eva et al. 1986 as Ancylobacter tetraedralis comb. nov., Angulomicrobium amanitiforme Fritz et al. 2004 as Ancylobacter amanitiformis comb. nov., and Methylorhabdus multivorans Doronina et al. 1996 as Ancylobacter multivorans comb. nov., and emended description of the genus Ancylobacter

Three novel facultatively methylotrophic bacteria, strains 3C^T, 1A, 8P, were isolated from activated sludges. The isolates were aerobic, Gram-stain-negative, non-motile, non-spore forming rods multiplying by binary fission. The predominant polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethylethanolamine, phosphatidylmonomethylethanolamine, and diphosphatidylglycerol. The major fatty acids of cells were С_18:1ω7c, C_19:0ω8c cyclo and C_16:0. Levels of 16S rRNA gene similarity indicates that the closely relatives are representatives of the genera Starkeya, Ancylobacter, Angulomicrobium and Methylorhabdus (96.4-99.4%). Genomic comparisons of 3C^T and its closest relatives, S. novella DSM 506^T and S. koreensis Jip08^T, shared 87.3 and 86.8% nucleotide identity and 28.3 and 26.8% digital DNA-DNA hybridization values, respectively. The average amino acid identities between the strain 3C^T and representatives of Starkeya, Ancylobacter and Angulomicrobium were in the range of 75.6-84.3%, which combines these strains into a single genus and gives rise to their reclassification. Based on polyphasic analyses, the strains 3C^T, 1A, 8P represents a novel species of the genus Ancylobacter, for which the name Ancylobacter moscoviensis sp. nov. is proposed. The type strain is 3C^T (= VKM B-3218^T = KCTC 62336^T). Furthermore, we also suggested the reclassification of Starkeya novella as Ancylobacter novellus comb. nov., Starkeya koreensis as Ancylobacter koreensis comb. nov., Angulomicrobium tetraedrale as Ancylobacter tetraedralis comb. nov., Angulomicrobium amanitiforme as Ancylobacter amanitiformis comb. nov. and Methylorhabdus multivorans as Ancylobacter multivorans comb. nov. with the emended description of the genus Ancylobacter.

Bacterioplankton Associated with Toxic Cyanobacteria Promote Pisum sativum (Pea) Growth and Nutritional Value through Positive Interactions

Research on Plant Growth-Promoting Bacteria (PGPB) has focused much more on rhizospheric bacteria. However, PGPB associated with toxic cyanobacterial bloom (TCB) could enter the rhizosphere through irrigation water, helping plants such as Pisum sativum L. (pea) overcome oxidative stress induced by microcystin (MC) and improve plant growth and nutritional value. This study aimed to isolate bacteria associated with toxic cyanobacteria, test PGPB properties, and inoculate them as a consortium to pea seedlings irrigated with MC to investigate their role in plant protection as well as in improving growth and nutritional value. Two bacterioplankton isolates and one rhizosphere isolate were isolated and purified on a mineral salt medium supplemented with 1000 μg/L MC and identified via their 16S rRNA gene. The mixed strains were inoculated to pea seedlings in pots irrigated with 0, 50, and 100 μg/L MC. We measured the morphological and physiological parameters of pea plants at maturity and evaluated the efficiency of the plant’s enzymatic and non-enzymatic antioxidant responses to assess the role and contribution of PGPB. Both bacterioplankton isolates were identified as Starkeya sp., and the rhizobacterium was identified as Brevundimonas aurantiaca. MC addition significantly (p < 0.05) reduced all the growth parameters of the pea, i.e., total chlorophyll content, leaf quantum yield, stomatal conductance, carotenoids, and polyphenol contents, in an MC concentration-dependent manner, while bacterial presence positively affected all the measured parameters. In the MC treatment, the levels of the pea’s antioxidant traits, including SOD, CAT, POD, PPO, GST, and ascorbic acid, were increased in the sterile pots. In contrast, these levels were reduced with double and triple PGPB addition. Additionally, nutritional values such as sugars, proteins, and minerals (Ca and K) in pea fruits were reduced under MC exposure but increased with PGPB addition. Overall, in the presence of MC, PGPB seem to positively interact with pea plants and thus may constitute a natural alternative for soil fertilization when irrigated with cyanotoxin-contaminated water, increasing the yield and nutritional value of crops.

Bacterial Biopolymer: Its Role in Pathogenesis to Effective Biomaterials

Bacteria are considered as the major cell factories, which can effectively convert nitrogen and carbon sources to a wide variety of extracellular and intracellular biopolymers like polyamides, polysaccharides, polyphosphates, polyesters, proteinaceous compounds, and extracellular DNA. Bacterial biopolymers find applications in pathogenicity, and their diverse materialistic and chemical properties make them suitable to be used in medicinal industries. When these biopolymer compounds are obtained from pathogenic bacteria, they serve as important virulence factors, but when they are produced by non-pathogenic bacteria, they act as food components or biomaterials. There have been interdisciplinary studies going on to focus on the molecular mechanism of synthesis of bacterial biopolymers and identification of new targets for antimicrobial drugs, utilizing synthetic biology for designing and production of innovative biomaterials. This review sheds light on the mechanism of synthesis of bacterial biopolymers and its necessary modifications to be used as cell based micro-factories for the production of tailor-made biomaterials for high-end applications and their role in pathogenesis.

Biochemical tests to determine the biodegradability potential of bacterial strains in PAH polluted sites

Although the use of degrading-bacteria is one of the most efficient methods for the bioremediation of polluted sites, detection, selection and proliferation of the most efficient and competing bacteria is still a challenge. The objective of this multi-stage research was to investigate the effects of the selected bacterial strains on the degradation of anthracene, florentine, naphthalene, and oil, determined by biochemical tests. In the first stage, using the following tests: (a) biosurfactant production (emulsification, oil spreading, number of drops, drop collapse, and surface tension), (b) biofilm production, (c) activity of laccase enzyme, and (d) exopolysaccaride production, the three bacterial strains with the highest degrading potential including Bacillus pumilus, B. aerophilus, and Marinobacter hydrocarbonoclasticus were chosen. In the second stage using the following tests: (a) bacterial growth, (b) laccase enzyme activity, and (c) biosurfactant production (emulsification, oil spreading, and collapse of droplet) the degrading ability of the three selected bacterial strains plus Escherichia coli were compared. Different bacterial strains were able to degrade anthracene, florentine, naphthalene, and oil by the highest rate, three days after inoculation (DAI). However, M. hydrocarbonoclasticus showed the highest rate of florentine degradation. Although with increasing pollutant concentration the degrading potential of the bacterial strains significantly decreased, M. hydrocarbonoclasticus was determined as the most efficient bacterial strain.

Molecular biological methods in environmental engineering

Microbes are sensitive to environmental changes and can respond in a short time. Genomics, proteomics, transcriptomics, metabolomics, and multigroup association are used to characterize the composition, function, and metabolism of microorganisms, and to evaluate the environment according to the changes in microorganisms, which has important reference and guiding significance of environmental monitoring, management, and repair. In this paper, the application of molecular biological methods to study environmental microorganisms in the fields of wastewater treatment, pollution control, soil improvement, and environmental monitoring in 2019 is reviewed.

Bacterial nanocellulose from agro-industrial wastes: low-cost and enhanced production by Komagataeibacter saccharivorans MD1

Bacterial nanocellulose (BNC) has been drawing enormous attention because of its versatile properties. Herein, we shed light on the BNC production by a novel bacterial isolate (MD1) utilizing various agro-industrial wastes. Using 16S rRNA nucleotide sequences, the isolate was identified as Komagataeibacter saccharivorans MD1. For the first time, BNC synthesis by K. saccharivorans MD1 was investigated utilizing wastes of palm date, fig, and sugarcane molasses along with glucose on the Hestrin-Schramm (HS) medium as a control. After incubation for 168 h, the highest BNC yield was perceived on the molasses medium recording 3.9 g/L with an initial concentration of (v/v) 10%. The physicochemical characteristics of the BNC sheets were inspected adopting field-emission scanning electron microscope (FESEM), atomic force microscopy (AFM), X-ray diffraction (XRD), and Fourier transform infrared (FTIR) analysis. The FESEM characterization revealed no impact of the wastes on either fiber diameter or the branching scheme, whereas the AFM depicted a BNC film with minimal roughness was generated using date wastes. Furthermore, a high crystallinity index was estimated by XRD up to 94% for the date wastes-derived BNC, while the FTIR analyses exhibited very similar profiles for all BNC films. Additionally, mechanical characteristics and water holding capacity of the produced BNCs were studied. Our findings substantiated that expensive substrates could be exchanged by agro-industrial wastes for BNC production conserving its remarkable physical and microstructural properties.

Bacterial nanocellulose production from naphthalene

Polycyclic aromatic compounds (PAHs) are toxic compounds that are released in the environment as a consequence of industrial activities. The restoration of PAH-polluted sites considers the use of bacteria capable of degrading aromatic compounds to carbon dioxide and water. Here we characterize a new Xanthobacteraceae strain, Starkeya sp. strain N1B, previously isolated during enrichment under microaerophilic conditions, which is capable of using naphthalene crystals as the sole carbon source. The strain produced a structured biofilm when grown on naphthalene crystals, which had the shape of a half-sphere organized over the crystal. Scanning electron microscopy (SEM) and GC-MS analysis indicated that the biofilm was essentially made of cellulose, composed of several micron-long nanofibrils of 60 nm diameter. A cellulosic biofilm was also formed when the cells grew with glucose as the carbon source. Fourier transformed infrared spectroscopy (FTIR) confirmed that the polymer was type I cellulose in both cases, although the crystallinity of the material greatly depended on the carbon source used for growth. Using genome mining and mutant analysis, we identified the genetic complements required for the transformation of naphthalene into cellulose, which seemed to have been successively acquired through horizontal gene transfer. The capacity to develop the biofilm around the crystal was found to be dispensable for growth when naphthalene was used as the carbon source, suggesting that the function of this structure is more intricate than initially thought. This is the first example of the use of toxic aromatic hydrocarbons as the carbon source for bacterial cellulose production. Application of this capacity would allow the remediation of a PAH into such a value-added polymer with multiple biotechnological usages.