Arsenic resistance genes of As-resistant purple nonsulfur bacteria isolated from As-contaminated sites for bioremediation application

Anoxygenic phototrophic purple non-sulfur bacteria: tool for bioremediation of hazardous environmental pollutants

The extraordinary metabolic flexibility of anoxygenic phototrophic purple non-sulfur bacteria (PNSB) has been exploited in the development of various biotechnological applications, such as wastewater treatment, biohydrogen production, improvement of soil fertility and plant growth, and recovery of high-value compounds. These versatile microorganisms can also be employed for the efficient bioremediation of hazardous inorganic and organic pollutants from contaminated environments. Certain members of PNSB, especially strains of Rhodobacter sphaeroides and Rhodopseudomonas palustris, exhibit efficient remediation of several toxic and carcinogenic heavy metals and metalloids, such as arsenic, cadmium, chromium, and lead. PNSB are also known to utilize diverse biomass-derived lignocellulosic organic compounds and xenobiotics. Although biodegradation of some substituted aromatic compounds by PNSB has been established, available information on the involvement of PNSB in the biodegradation of toxic organic pollutants is limited. In this review, we present advancements in the field of PNSB-based bioremediation of heavy metals and organic pollutants. Furthermore, we highlight that the potential role of PNSB as a promising bioremediation tool remains largely unexplored. Thus, this review emphasizes the necessity of investing extensive research efforts in the development of PNSB-based bioremediation technology.

Effects of LPS from Rhodobacter sphaeroides, a Purple Non-Sulfur Bacterium (PNSB), on the Gene Expression of Rice Root

The effects of lipopolysaccharide (LPS) from Rhodobacter sphaeroides, a purple non-sulfur bacterium (PNSB), on the gene expression of the root of rice (Oryza sativa) were investigated by next generation sequencing (NGS) RNA-seq analysis. The rice seeds were germinated on agar plates containing 10 pg/mL of LPS from Rhodobacter sphaeroides NBRC 12203 (type culture). Three days after germination, RNA samples were extracted from the roots and analyzed by RNA-seq. The effects of dead (killed) PNSB cells of R. sphaeroides NBRC 12203^T at the concentration of 10¹ cfu/mL (ca. 50 pg cell dry weight/mL) were also examined. Clean reads of NGS were mapped to rice genome (number of transcript ID: 44785), and differentially expressed genes were analyzed by DEGs. As a result of DEG analysis, 300 and 128 genes, and 86 and 8 genes were significantly up- and down-regulated by LPS and dead cells of PNSB, respectively. The plot of logFC (fold change) values of the up-regulated genes of LPS and PNSB dead cells showed a significant positive relationship (r² = 0.6333, p < 0.0001), indicating that most of the effects of dead cell were attributed to those of LPS. Many genes related to tolerance against biotic (fungal and bacterial pathogens) and abiotic (cold, drought, and high salinity) stresses were up-regulated, and the most strikingly up-regulated genes were those involved in the jasmonate signaling pathway, and the genes of chalcone synthase isozymes, indicating that PNSB induced defense response against biotic and abiotic stresses via the jasmonate signaling pathway, despite the non-pathogenicity of PNSB.

Microbial biochemical pathways of arsenic biotransformation and their application for bioremediation

Arsenic is a ubiquitous toxic metalloid, the concentration of which is beyond WHO safe drinking water standards in many areas of the world, owing to many natural and anthropogenic activities. Long-term exposure to arsenic proves lethal for plants, humans, animals, and even microbial communities in the environment. Various sustainable strategies have been developed to mitigate the harmful effects of arsenic which include several chemical and physical methods, however, bioremediation has proved to be an eco-friendly and inexpensive technique with promising results. Many microbes and plant species are known for arsenic biotransformation and detoxification. Arsenic bioremediation involves different pathways such as uptake, accumulation, reduction, oxidation, methylation, and demethylation. Each of these pathways has a certain set of genes and proteins to carry out the mechanism of arsenic biotransformation. Based on these mechanisms, various studies have been conducted for arsenic detoxification and removal. Genes specific for these pathways have also been cloned in several microorganisms to enhance arsenic bioremediation. This review discusses different biochemical pathways and the associated genes which play important roles in arsenic redox reactions, resistance, methylation/demethylation, and accumulation. Based on these mechanisms, new methods can be developed for effective arsenic bioremediation.

Recent progress in the use of purple non-sulfur bacteria as probiotics in aquaculture

The use of probiotics in aquaculture is widely recognized as an ecological and cost-effective approach to raising healthy, pathogen-tolerant aquatic animals, including fish and shrimp. In particular for shrimp, probiotics are viewed as a promising countermeasure to the recent severe damage to the shrimp industry by bacterial and viral pathogens. Purple non-sulfur bacteria (PNSB) are Gram-negative, non-pathogenic bacteria with wide application potential in agriculture, wastewater treatment, and bioenergy/biomaterials production. In aquaculture, lactic bacteria and Bacillus are the major probiotic bacteria used, but PNSB, like Rhodopseudomonas and Rhodobacter, are also used. In this review, we summarize the previous work on the use of PNSB in aquaculture, overview the previous studies on the stimulation of innate immunity of shrimp by various probiotic microorganisms, and also share our results in the probiotic performance of Rhodovulum sulfidophilum KKMI01, a marine PNSB, which showed a superior effect in promotion of growth and stimulation of immunity in shrimp at a quite low concentration of 1 × 10³ cfu (colony forming unit)/ml in rearing water.

Advances in bioleaching of waste lithium batteries under metal ion stress

In modern societies, the accumulation of vast amounts of waste Li-ion batteries (WLIBs) is a grave concern. Bioleaching has great potential for the economic recovery of valuable metals from various electronic wastes. It has been successfully applied in mining on commercial scales. Bioleaching of WLIBs can not only recover valuable metals but also prevent environmental pollution. Many acidophilic microorganisms (APM) have been used in bioleaching of natural ores and urban mines. However, the activities of the growth and metabolism of APM are seriously inhibited by the high concentrations of heavy metal ions released by the bio-solubilization process, which slows down bioleaching over time. Only when the response mechanism of APM to harsh conditions is well understood, effective strategies to address this critical operational hurdle can be obtained. In this review, a multi-scale approach is used to summarize studies on the characteristics of bioleaching processes under metal ion stress. The response mechanisms of bacteria, including the mRNA expression levels of intracellular genes related to heavy metal ion resistance, are also reviewed. Alleviation of metal ion stress via addition of chemicals, such as spermine and glutathione is discussed. Monitoring using electrochemical characteristics of APM biofilms under metal ion stress is explored. In conclusion, effective engineering strategies can be proposed based on a deep understanding of the response mechanisms of APM to metal ion stress, which have been used to improve bioleaching efficiency effectively in lab tests. It is very important to engineer new bioleaching strains with high resistance to metal ions using gene editing and synthetic biotechnology in the near future.

Special Issue “Biotechnological Application of Photosynthetic Bacteria”

This Special Issue aims to contribute to the current knowledge in the field and promote the practical application of photosynthetic bacteria (PSB) biotechnology [...]

Effects of Seed Bio-Priming by Purple Non-Sulfur Bacteria (PNSB) on the Root Development of Rice

The effects of seed bio-priming (seed soaking) with purple non-sulfur bacteria (PNSB) on the grain productivity and root development of rice were examined by a field study and laboratory experiments, respectively. Two PNSB strains, Rhodopseudomonas sp. Tsuru2 and Rhodobacter sp. Tsuru3, isolated from the paddy field of the study site were used for seed bio-priming. For seed bio-priming in the field study, the rice seeds were soaked for 1 day in water containing a 1 × 10⁵ colony forming unit (cfu)/mL of PNSB cells, and the rice grain productivities at the harvest time were 420, 462 and 504 kg/are for the control, strain Tsuru2-primed, and strain Tsuru3-primed seeds, respectively. The effects of seed priming on the root development were examined with cell pot cultivation experiments for 2 weeks. The total root length, root surface area, number of tips and forks were evaluated with WinRhizo, an image analysis system, and strains Tsuru2- and Tsuru3-primed seeds showed better root development than the control seeds. The effects of seed priming with the dead (killed) PNSB cells were also examined, and the seed priming with the dead cells was also effective, indicating that the effects were attributed to some cellular components. We expected the lipopolysaccharide (LPS) of PNSB as the effective component of PNSB and found that seed priming with LPS of Rhodobacter sphaeroides NBRC 12203 (type culture) at the concentrations of 5 ng/mL and 50 ng/mL enhanced the root development.

Soil ridge cultivation maintains grain As and Cd at low levels and inhibits As methylation by changing arsM-harboring bacterial communities in paddy soils

The simultaneous mitigation of toxic arsenic (As) and cadmium (Cd) in rice grain remains a global challenge. The over-accumulation of husk dimethylarsinic acid (DMAs) induces the rice straight-head disease, which threatens rice production worldwide. In this study, we investigated various soil ridge height treatments with Eh ranging from - 225-87 mV and pH ranging from 6.3 to 4.1. Soil ridge cultivation can maintain grain As and Cd at low levels for slightly co-contaminated paddy soils, especially when the ridge height is 11 cm (Eh of 43 mV and pH of 4.6), where grain inorganic As decreased-at maximum-by 48% and DMAs by 55%. Grain Cd (0.14 mg kg^-1) increased but was still below the limit (0.2 mg kg^-1) in China, and the cost of ridging is acceptable. There were definite correlations among porewater As, Cd, Fe, S, and Mn contents across various Eh and pH values. Soil ridge cultivation significantly (P < 0.05) diminished the copy number of As-reducing (harboring arsC and arrA), As-methylating (harboring arsM), and sulfate-reducing (harboring dsrA) bacteria. Moreover, soil ridge cultivation shifted the arsM-harboring microbiota. In response to ridge height increase, the abundance of the bacterial biomarker phylum Euryachaeota declined and the families Halorubrum and Planctomyces were gradually replaced by Sandaracinus in paddy soil.

Biotransformation and removal of arsenic oxyanions by Alishewanella agri PMS5 in biofilm and planktonic states

Arsenic oxyanions are toxic chemicals that impose a high risk to humans and other living organisms in the environment. The present study investigated indigenous heterotrophic bacteria in the tailings dam effluent (TDE) of a gold mining factory. Thirty-seven arsenic resistant bacteria were cultured on Reasoner's 2A agar supplemented with arsenic salts through filtration. One strain encoded as PMS5 with the highest resistance to 140-mM sodium arsenite and 600-mM sodium arsenate in tryptic soy broth was selected for further investigations. According to phenotypic examinations and 16S rDNA sequence analysis, PMS5 belonged to the genus Alishewanella and was sensitive to most of the examined antibiotics. The biosorption and bioaccumulation abilities of arsenic salts were observed in this isolate based on Scanning Electron Microscopy (SEM) with Energy Dispersive X-Ray Analysis (EDX) and biosorption and bioaccumulation data. PMS5 was also found to cause the volatilization and biotransformation of arsenic oxyanions through their oxidation and reduction. Moreover, the contribution of PMS5 to arsenic (3⁺, 5⁺) bioprocessing under oligotrophic conditions was confirmed in fixed-bed reactors fed with the TDE of the gold factory (R1) and synthetic water containing As⁵⁺ (R2). According to biofilm assays such as biofilm staining, cell count, detachment assay and SEM, the arsenic significantly reduced the biofilm density of the examined reactors compared to that of the control (R3). Arsenate reduction and arsenite oxidation under bioreactor conditions were respectively obtained as 75.5-94.7% and 8%. Furthermore, negligible arsenic volatilization (1.2 ppb) was detected.

Screening of plant growth promoting attributes and arsenic remediation efficacy of bacteria isolated from agricultural soils of Chhattisgarh

Arsenic (As) resistant indigenous bacteria with discrete minimum inhibitory concentration values for arsenate [As(V)] and arsenite [As(III)] were isolated from the paddy fields of different regions of Chhattisgarh, India, following enrichment culture technique. Evaluation of the plant growth promoting (PGP) properties of the isolates revealed that two rod-shaped Gram-positive bacteria viz., ARP2 and ART2 acquired various PGP traits, including phosphate solubilization, production of siderophore, indole acetic acid, ammonia, and exopolysaccharide. Both the isolates significantly increased (40-80%) the root length of Oryza sativa L. even under As-exposure. Sequencing of 16S rRNA gene identified these isolates as Bacillus nealsonii strain ARP2 and Bacillus tequilensis strain ART2, respectively. Isolate ARP2 exhibited arsenate reductase activity thereby rapidly reduced As(V) into As(III), achieving a reduction rate of 37.5 μM min^-1. Alike, strain ART2 was capable of oxidizing As(III) into As(V) via arsenite oxidase enzyme, and revealed the oxidation rate of 21.8 μM min^-1. Quantitative estimation of As through atomic absorption spectrophotometer revealed that the isolates ARP2 and ART2 removed 93 ± 0.2% and 77 ± 0.14% of As(V) and As(III), respectively, from As-containing culture media. The FTIR analysis showed the interaction of As with the cell membrane and was further confirmed by SEM and TEM techniques, which marked the increase in cell volume owing to successive accumulation of As. The As-resistant and PGP properties of above two isolates demonstrates their potentiality for sustainable bioremediation of As, and establishment of flora in As-rich environment.

Study of As-resistant bacteria from Nadia, India and a survey of two As resistance-related proteins

The present investigation deals with the characterisation of three As-resistant bacteria, Bacillus aryabhattai strain VPS1, Bacillus licheniformis strain VPS6 and Sporosarcina thermotolerans strain VPS7 isolated from the rhizosphere of a contaminated paddy field in Chakdaha, Nadia, West Bengal, India. Two strains, VPS6 and VPS7 showed ureolytic activity, which can be used for microbial-induced calcite precipitation of As as a bioremediation option. However, As reduction and oxidation capacities were not reported in any of these bacteria. A phylogenetic tree of 16S ribosomal RNA gene sequences was constructed for all three bacterial isolates, including different species of As-resistant Bacillus and Sporosarcina. Furthermore, literature survey and genome mining were employed to explore the diversity of As resistance-related proteins, arsenite S-adenosylmethyltransferase (ArsM) and arsenical pump membrane protein (ArsB) among different bacteria, and the phylogenetic relatedness was studied to understand the distribution and evolution of their amino acid sequences. ArsB was predominantly present in a wide variety of bacteria (347 taxa); however, ArsM was reported in comparatively fewer isolates (109 taxa). There were a total of 60 similar taxa that contained both ArsM and ArsB. Both proteins were most abundantly present in phylum Proteobacteria. Overall, this investigation enumerates As-resistant bacteria to understand the As metabolism in the environment, and the phylogenetic analysis of As resistance-related proteins helps in understanding the functional relationship in different bacteria for their role in As mobility in the environment.

Arsenic respiration and detoxification by purple non-sulphur bacteria under anaerobic conditions

Two arsenic-resistant purple non-sulphur bacteria (PNSB), Q3B and Q3C, were isolated (from industrial contaminated site and paddy fields) and identified by SSU rRNA gene sequencing as Rhodospirillum and Rhodospirillaceae species, respectively. Maximum arsenic reduction by these PNSB was observed in anaerobic conditions. Rhodospirillum sp. Q3B showed 74.92% (v/v) arsenic reduction while Rhodospirillaceae sp. Q3C reduced arsenic up to 76.67% (v/v) in anaerobic conditions. Rhodospirillaceae sp. Q3C was found to contain highest carotenoid content up to 5.6mg·g^-1. Under anaerobic conditions, the isolates were able to respire arsenic in the presence of lactate, citrate, and oxalate. Rhodospirillum sp. Q3B and Rhodospirillaceae sp. Q3C were also found to produce hydrogen gas. Such diverse bacteria can be useful tools for bioremediation purposes. These bacteria can be further exploited and optimized to treat wastewater containing arsenic along with bio-hydrogen production.

Metagenomic Evidence for a Methylocystis Species Capable of Bioremediation of Diverse Heavy Metals

Heavy metal pollution has become an increasingly serious problem worldwide. Co-contamination with toxic mercury (Hg) and arsenic (As) presents a particularly difficult bioremediation trouble. By oxidizing the greenhouse gas methane, methanotrophs have been demonstrated to have high denitrification activity in eutrophic waters, indicating their possible potential for use in bioremediation of Hg(II) and As(V) in polluted water. Using metagenomics, a novel Methylocystis species (HL18), which was one of the most prevalent bacteria (9.9% of the relative abundance) in a CH₄-based bio-reactor, is described here. The metagenomic-assembled genome (MAG) HL18 had gene products whose average amino acid identity against other known Methylocystis species varied from 69 to 85%, higher than the genus threshold but lower than the species boundary. Genomic analysis indicated that HL18 possessed all the genes necessary for the reduction of Hg(II) and As(V). Phylogenetic investigation of mercuric reductase (MerA) found that the HL18 protein was most closely affiliated with proteins from two Hg(II)-reducing bacteria, Bradyrhizobium sp. strain CCH5-F6 and Paracoccus halophilus. The genomic organization and phylogeny of the genes in the As(V)-reducing operon (arsRCCB) had significant identity with those from a As(V)-reducing bacterium belonging to the Rhodopseudomonas genus, indicating their reduction capability of As(V). Further analysis found that at least eight genera of methanotrophs possess both Hg(II) and As(V) reductases, illustrating the generally overlooked metabolic potential of methanotrophs. These results suggest that methanotrophs have greater bioremediation potential in heavy metal contaminated water than has been appreciated and could play an important role in the mitigation of heavy metal toxicity of contaminated wastewater.

Reduction in arsenic toxicity and uptake in rice (Oryza sativa L.) by As-resistant purple nonsulfur bacteria

This study aimed to investigate the potential of Rhodopseudomonas palustris C1 and Rubrivivax benzoatilyticus C31 to ameliorate As toxicity and to reduce As uptake in rice. Strain C1 was superior to strain C31 for siderophore production. The mixed culture (1: 1) was most effective in reducing the toxicity of As species [As(III) and/or As(V), each 30 mg/l] by yielding maximal germination index that related to α- and β-amylase activities in two Thai rice cultivars (HomNil: HN and PathumThani 1: PT). Arsenic toxicity to the seed germination followed the order: mixed As species > As(III) > As(V); and the toxicity was reduced in inoculated sets, particularly with a mixed culture. The mixed culture significantly enhanced rice growth under As stress in both rice cultivars as indicated by an increase in the production of chlorophyll a and b, and also supporting the non-enzymatic (carotenoids, lipid oxidation, and nitric oxide) and enzymatic (superoxide dismutase, ascorbate peroxidase, catalase, and glutathione reductase) activities. These were concomitant with productions of 5-aminolevulinic acid, indole-3-acetic acid, exopolymeric substances, and siderophores which significantly reduced As accumulation in treated rice. It can be concluded that the mixed culture has great potential to ameliorate rice from As toxicity by preventing As species entry into rice for enhancing rice growth and also for reducing As accumulation to produce safe rice from rice grown in contaminated paddy fields.