Acetonitrile degradation under haloalkaline conditions by Natronocella acetinitrilica gen. nov., sp. nov

Extending the benefits of PGPR to bioremediation of nitrile pollution in crop lands for enhancing crop productivity

Incessant release of nitrile group of compounds such as cyanides into agricultural land through industrial effluents and excessive use of nitrile pesticides has resulted in increased nitrile pollution. Release of nitrile compounds (NCs) as plant root exudates is also contributing to the problem. The released NCs interact with soil elements and persists for a long time. Persistent higher concentration of NCs in soil cause toxicity to beneficial microflora and affect crop productivity. The NCs can cause more problems to human health if they reach groundwater and enter the food chain. Nitrile degradation by soil bacteria can be a solution to the problem if thoroughly exploited. However, the impact of such bacteria in plant and soil environments is still not properly explored. Plant growth-promoting rhizobacteria (PGPR) with nitrilase activity has recently gained attention as potential solution to address the problem. This paper reviews the core issue of nitrile pollution in soil and the prospects of application of nitrile degrading bacteria for soil remediation, soil health improvement and plant growth promotion in nitrile-polluted soils. The possible mechanisms of PGPR that can be exploited to degrade NCs, converting them into plant useful compounds and synthesis of the phytohormone IAA from degraded NCs are also discussed at length.

Natural Products Containing the Nitrile Functional Group and Their Biological Activities

The importance of nitriles as a key class of chemicals with applications across the sciences is widely appreciated. The natural world is an underappreciated source of chemically diverse nitriles. With this in mind, this review describes novel nitrile-containing molecules isolated from natural sources from 1998 to 2021, as well as a discussion of the biological activity of these compounds. This study gathers 192 molecules from varied origins across the plant, animal, and microbial worlds. Their biological activity is extremely diverse, with many potential medicinal applications.

Genomic Comparison, Phylogeny and Taxonomic Reevaluation of the Ectothiorhodospiraceae and Description of Halorhodospiraceae fam. nov. and Halochlorospira gen. nov

The Ectothiorhodospiraceae family represents purple sulfur bacteria of the Gammaproteobacteria found primarily in alkaline soda lakes of moderate to extremely high salinity. The main microscopically visible characteristic separating them from the Chromatiaceae is the excretion of the intermediate elemental sulfur formed during oxidation of sulfide prior to complete oxidation to sulfate rather than storing it in the periplasm. We present a comparative study of 38 genomes of all species of phototrophic Ectothiorhodospiraceae. We also include a comparison with those chemotrophic bacteria that have been assigned to the family previously and critically reevaluate this assignment. The data demonstrate the separation of Halorhodospira species in a major phylogenetic branch distant from other Ectothiorhodospiraceae and support their separation into a new family, for which the name Halorhodospiraceae fam. nov. is proposed. In addition, the green-colored, bacteriochlorophyll-containing species Halorhodospira halochloris and Halorhodospira abdelmalekii were transferred to the new genus Halochlorospira gen. nov. of this family. The data also enable classification of several so far unclassified isolates and support the separation of Ectothiorhodospira shaposhnikovii and Ect. vacuolata as well as Ect. mobilis and Ect. marismortui as distinct species.

Different acetonitrile degraders and degrading genes between anaerobic ammonium oxidation and sequencing batch reactor as revealed by stable isotope probing and magnetic-nanoparticle mediated isolation

Microbial degraders play crucial roles in wastewater treatment processes, but their use is limited as most microbes are yet unculturable. Stable isotope probing (SIP) is a cultivation-independent technique identifying functional-yet-uncultivable microbes in ambient environment, but is unsatisfactory for substrates with low assimilation rate owing to the low isotope incorporation into DNA. In this study, we used acetonitrile as the target low-assimilation chemical in many wastewater treatment plants and attempted to identify the active acetonitrile degraders in the activated sludge, via DNA-SIP and magnetic-nanoparticle mediated isolation (MMI) which is another cultivation-independent approach without the requirement of substrate labeling. The two approaches identified different active acetonitrile degraders in a 3-day short-term anaerobic ammonium oxidation (ANAMMOX). MMI enriched significantly more acetonitrile-degraders than SIP, showing the advantages in identifying the active degraders for low-assimilation substrates. Sequencing batch reactor (SBR, 30-day degradation) helped in more incorporation of ¹⁵N-labeled acetonitrile into the active degraders, thus the same acetonitrile-degraders and acetonitrile-degrading genes were identified by SIP and MMI. Different acetonitrile degraders between ANAMMOX and SBR were attributed to the distinct hydrological conditions. Our study for the first time explored the succession of acetonitrile-degraders in wastewater and identified the active acetonitrile-degraders which could be further enriched for enhancing acetonitrile degradation performance. These findings provide new insights into the acetonitrile metabolic process in wastewater treatment plants and offer suggestive conclusions for selecting appropriate treatment strategy in wastewater management.

Exploitation of Potential Extremophiles for Bioremediation of Xenobiotics Compounds: A Biotechnological Approach

Microorganisms that are capable of live and adapt in hostile habitats of different environmental factors such as extremes temperature, salinity, nutrient availability and pressure are known as extremophiles. Exposure to xenobiotic compounds is global concern influencing the world population as a health hazard. Hence their removal is warranted using biological means that is very sustainable, potentially cost-effective and eco-friendly. Due to adaptation in extreme environments and unique defense mechanisms, they are receiving more attention for the bioremediation of the xenobiotic compounds. They possess robust enzymatic and biocatalytic systems that make them suitable for the effective removal of pollutants from the contaminated environment. Additionally, the extremophiles act as microfactories having specific genetic and biotechnological potential for the production of biomolecules. This mini review will provide an overview of microbial degradation metabolic pathways for bioremediation along with the molecular and physiological properties of diverse extremophiles from variety of habitats. Furthermore, the factors affecting the bioremediation process is also summarized.

Biodegradation of butyronitrile and demonstration of its mineralization by Rhodococcus sp. MTB5

A nitrile utilizing bacterium Rhodococcus sp. MTB5 was previously isolated in our laboratory by the enrichment culture technique. It is able to utilize butyronitrile as sole carbon, nitrogen, and energy source. Maximum butyronitrile degrading property of this strain has been investigated. Results reveal that 100, 98, and 88 % degradation was achieved for 2, 2.5, and 3 % butyronitrile, respectively. The strain is capable of growing in as high as 5 % butyronitrile concentration. A two-step pathway involving nitrile hydratase (NHase) and amidase was observed for the biodegradation of butyronitrile. Complete degradation (mineralization) of butyronitrile with the help of metabolite feeding experiment was reported. The significance of this investigation was the capability of the strain to completely degrade and its ability to grow on higher concentrations of butyronitrile. These potential features make it a suitable candidate for practical field application for effective in situ bioremediation of butyronitrile contaminated sites.

Halopeptonella vilamensis gen. nov, sp. nov., a halophilic strictly aerobic bacterium of the family Ectothiorhodospiraceae

A Gram-negative, halophilic, heterotrophic, rod-shaped, non-spore-forming bacterium (SV525T) was isolated from the sediment of a hypersaline lake located at 4600 m above sea level (Laguna Vilama, Argentina). Strain SV525T was strictly aerobic and formed pink-to-magenta colonies. Growth occurred at 10–35 °C (optimum 25–30 °C), at pH levels 6.0–8.5 (optimum 7.0) and at NaCl concentrations of 7.5–25 % (w/v) with an optimum at 10–15 % (w/v). The strain required sodium and magnesium but not potassium ions for growth. Grows with tryptone, or Bacto Peptone as sole carbon and energy source and requires yeast extract for growth. It produced catalase and oxidase. The predominant ubiquinone was Q-8 and the major fatty acids comprised C18:1 ω7c, C16:0 and C18:0. The DNA G+C content was 60.4 mol% and its polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and a phosphoglycolipid. Phylogenetic analysis based on 16S rRNA gene indicated that strain SV525T belongs to the family Ectothiorhodospiraceae within the class Gammaproteobacteria. On the basis of phylogenetic and phenotypic data, SV525T represents a novel genus and species, for which the name Halopeptonella vilamensis gen. nov., sp. nov. is proposed. The type strain is SV525T (=DSM 21056T =JCM 16388T =NCIMB 14596T).

A novel strategy for acetonitrile wastewater treatment by using a recombinant bacterium with biofilm-forming and nitrile-degrading capability

There is a great need for efficient acetonitrile removal technology in wastewater treatment to reduce the discharge of this pollutant in untreated wastewater. In this study, a nitrilase gene (nit) isolated from a nitrile-degrading bacterium (Rhodococcus rhodochrous BX2) was cloned and transformed into a biofilm-forming bacterium (Bacillus subtilis N4) that expressed the recombinant protein upon isopropylthio-β-galactoside (IPTG) induction. The recombinant bacterium (B. subtilis N4-pHT01-nit) formed strong biofilms and had nitrile-degrading capability. Further testing demonstrated that biofilms formed by B. subtilis N4-pHT01-nit were highly resistant to loading shock from acetonitrile and almost completely degraded the initial concentration of acetonitrile (800 mg L(-1)) within 24 h in a moving bed biofilm reactor (MBBR) after operation for 35 d. The bacterial composition of the biofilm, identified by high-throughput sequencing, in a reactor in which the B. subtilis N4-pHT01-nit bacterium was introduced indicated that the engineered bacterium was successfully immobilized in the reactor and became dominant genus. This work demonstrates that an engineered bacterium with nitrile-degrading and biofilm-forming capacity can improve the degradation of contaminants in wastewater. This approach offers a novel strategy for enhancing the biological oxidation of toxic pollutants in wastewater.

Woeseia oceani gen. nov., sp. nov., a chemoheterotrophic member of the order Chromatiales, and proposal of Woeseiaceae fam. nov

A novel Gram-stain-negative, rods or bent rods, facultatively anaerobic, oxidase-negative and catalase-positive bacterium, designated XK5T, was isolated from coastal sediment from Xiaoshi Island, Weihai, China. Optimal growth occurred at 28-35 °C (range 8-42 °C) and pH 7.0-8.0 (range pH 6.0-9.0) with 1-3 % (w/v) NaCl (range 0.5-8 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain XK5T was 92.1 % similar to the type strain of Thioalkalivibrio thiocyanodenitrificans, 91.9 % to the type strain of Thioalkalivibrio sulfidiphilus and 91.8 % to the type strain of Thioalkalivibrio denitrificans; similarity to other species was less than 91 %. The isolate and closely related environmental clones formed a novel family level clade in the order Chromatiales. The polar lipid profile of the novel isolate consisted of phosphatidylethanolamine, phosphatidylglycerol and some other unknown phospholipids, aminolipids and lipids. Major cellular fatty acids were iso-C17 : 1ω9c and iso-C15 : 0 and the main respiratory lipoquinone was Q-8. The DNA G+C content of strain XK5T was 59.3 mol%. Comparative analysis of 16S rRNA gene sequences and characterization indicated that strain XK5T represents a novel species of a new genus within a novel family of the order Chromatiales, for which the name Woeseia oceani gen. nov., sp. nov. is proposed. The type strain of Woeseia oceani is XK5T ( = ATCC BAA-2615T = CICC 10905T). In addition, a novel family name, Woeseiaceae fam. nov., is proposed to accommodate the genus Woeseia.

Enzymatic degradation of aliphatic nitriles by Rhodococcus rhodochrous BX2, a versatile nitrile-degrading bacterium

Nitriles are common environmental pollutants, and their removal has attracted increasing attention. Microbial degradation is considered to be the most acceptable method for removal. In this work, we investigated the biodegradation of three aliphatic nitriles (acetonitrile, acrylonitrile and crotononitrile) by Rhodococcus rhodochrous BX2 and the expression of their corresponding metabolic enzymes. This organism can utilize all three aliphatic nitriles as sole carbon and nitrogen sources, resulting in the complete degradation of these compounds. The degradation kinetics were described using a first-order model. The degradation efficiency was ranked according to t1/2 as follows: acetonitrile>trans-crotononitrile>acrylonitrile>cis-crotononitrile. Only ammonia accumulated following the three nitriles degradation, while amides and carboxylic acids were transient and disappeared by the end of the assay. mRNA expression and enzyme activity indicated that the tested aliphatic nitriles were degraded via both the inducible NHase/amidase and the constitutive nitrilase pathways, with the former most likely preferred.

A combined approach to assess the microbial contamination of the archimedes palimpsest

A combined approach, using molecular and microscopic techniques, was used to identify the microbiota associated with the Archimedes Palimpsest, an unusual parchment manuscript. SEM analyses revealed the microbial damage to the collagen fibers and the presence of characteristic cell chains typical of filamentous bacteria and fungal spores. Molecular analysis confirmed a homogeneous bacterial community colonizing the manuscript. The phyla Proteobacteria and Actinobacteria were associated with this ancient parchment; the sequences were most related to uncultured clones detected in the human skin microbiome and in ephitelium, and to cultivated species of the genera Acinetobacter and Nocardiopsis. Nevertheless, a great variation was observed among the different sampled areas indicating fungal diversity. Blumeria spp. dominated in the healthy areas of the parchment while degraded areas showed disparate fungal communities, with dominant members of the genera Mucor and Cladosporium. In addition, the quantification of the β-actin gene by real-time PCR analyses (qPCR) revealed a higher fungal abundance on degraded areas than on the healthy ones.

How could haloalkaliphilic microorganisms contribute to biotechnology?

Haloalkaliphiles are microorganisms requiring Na+concentrations of at least 0.5 mol·L–1and an alkaline pH of 9 for optimal growth. Their unique features enable them to make significant contributions to a wide array of biotechnological applications. Organic compatible solutes produced by haloalkaliphiles, such as ectoine and glycine betaine, are correlated with osmoadaptation and may serve as stabilizers of intracellular proteins, salt antagonists, osmoprotectants, and dermatological moisturizers. Haloalkaliphiles are an important source of secondary metabolites like rhodopsin, polyhydroxyalkanoates, and exopolysaccharides that play essential roles in biogeocycling organic compounds. These microorganisms also can secrete unique exoenzymes, including proteases, amylases, and cellulases, that are highly active and stable in extreme haloalkaline conditions and can be used for the production of laundry detergent. Furthermore, the unique metabolic pathways of haloalkaliphiles can be applied in the biodegradation and (or) biotransformation of a broad range of toxic industrial pollutants and heavy metals, in wastewater treatment, and in the biofuel industry.

Simultaneous purification of nitrile hydratase and amidase of Alcaligenes sp. MTCC 10674

Alcaligenes sp. MTCC 10674 has a bienzymatic system for the hydrolysis of nitriles. The nitrile hydratase and amidase have been purified simultaneously to homogeneity using a combination of (NH)₄SO₄ precipitation, ion exchange chromatography and gel permeation chromatography. Nitrile hydratase and amidase have molecular weight of 47 and 114 kDa, respectively and exist as heterodimer. Optimum temperatures for maximum activity of nitrile hydratase and amidase were 15 °C (2.4 U/mg protein) and 45 °C (2.3 U/mg protein), respectively. Nitrile hydratase showed maximum 7.8 U/mg protein at 50 mM acrylonitrile and amidase has 9.2 U/mg protein at 25 mM propionamide. Nitrile hydratase has V_max 10 μmol/min/mg and K_m 40 mM, while amidase has V_max 12.5 μmol/min/mg and K_m 45.5 mM, respectively. Heavy metal ions Hg²⁺, Ag⁺, Pb²⁺ and Cu²⁺ were strong inhibitors of nitrile hydratase and amidase activity.

Immobilization of Rhodococcus rhodochrous BX2 (an acetonitrile-degrading bacterium) with biofilm-forming bacteria for wastewater treatment

In this study, a unique biofilm consisting of three bacterial strains with high biofilm-forming capability (Bacillus subtilis E2, E3, and N4) and an acetonitrile-degrading bacterium (Rhodococcus rhodochrous BX2) was established for acetonitrile-containing wastewater treatment. The results indicated that this biofilm exhibited strong resistance to acetonitrile loading shock and displayed a typical spatial and structural heterogeneity and completely depleted the initial concentration of acetonitrile (800mgL(-1)) within 24h in a moving-bed-biofilm reactor (MBBR) after operation for 30days. The immobilization of BX2 cells in the biofilm was confirmed by PCR-DGGE. It has been demonstrated that biofilm-forming bacteria can promote the immobilization of contaminant-degrading bacteria in the biofilms and can subsequently improve the degradation of contaminants in wastewater. This approach offers a novel strategy for enhancing biological oxidation of toxic pollutants in wastewater.

Energy from plants and microorganisms: progress in plant-microbial fuel cells

Plant-microbial fuel cells (PMFCs) are newly emerging devices, in which electricity can be generated by microorganisms that use root exudates as fuel. This review presents the development of PMFCs, with a summary of their power generation, configurations, plant types, anode and cathode materials, biofilm communities, potential applications, and future directions.

Biological neutralization of chlor-alkali industry wastewater

The present work reports biological neutralization of chlor-alkali industrial effluent by an alkaliphilic bacterium, isolated from the Gujarat coast, which was identified as Enterococcus faecium strain R-5 on the basis of morphological, biochemical and partial 16S rRNA gene sequencing. The isolate was capable of bringing down the pH of waste water from 12.0 to 7.0 within 3 h in the presence of carbon and nitrogen sources, with simultaneous reduction in total dissolved solutes (TDS) up to 19-22%. This bacterium produced carboxylic acid, as revealed by FT-IR analysis, which facilitated neutralization of alkaline effluent. The presence of unconventional raw materials viz. Madhuca indica flowers or sugar cane bagasse as carbon and nitrogen sources could effectively neutralize alkaline effluent and thus making the bioremediation process economically viable. The time required for neutralization varied with size of inoculum. To the best of our knowledge, this is the first report on biological neutralization of a chlor-alkali industrial effluent.

Characterization of acetonitrile-tolerant marine bacterium Exiguobacterium sp. SBH81 and its tolerance mechanism

A Gram-positive marine bacterium, Exiguobacterium sp. SBH81, was isolated as a hydrophilic organic-solvent tolerant bacterium, and exhibited high tolerance to various types of toxic hydrophilic organic solvents, including acetonitrile, at relatively high concentrations (up to 6% [v/v]) under the growing conditions. Investigation of its tolerance mechanisms illustrated that it does not rely on solvent inactivation processes or modification of cell surface characteristics, but rather, increase of the cell size lowers solvent partitioning into cells and the extrusion of solvents through the efflux system. A test using efflux pump inhibitors suggested that secondary transporters, i.e. resistance nodulation cell division (RND) and the multidrug and toxic compound extrusion (MATE) family, are involved in acetonitrile tolerance in this strain. In addition, its acetonitrile tolerance ability could be stably and significantly enhanced by repetitive growth in the presence of toxic acetonitrile. The marked acetonitrile tolerance of Exiguobacterium sp. SBH81 indicates its potential use as a host for biotechnological fermentation processes as well as bioremediation.

Plasticicumulans acidivorans gen. nov., sp. nov., a polyhydroxyalkanoate-accumulating gammaproteobacterium from a sequencing-batch bioreactor

Here, we describe a novel bacterium, strain TUD-YJ37T, which can accumulate polyhydroxybutyrate (PHB) to more than 85 % (w/w) dry cell weight. The bacterium was isolated from a mixed-culture bioreactor by using a feast–famine regime and its properties were characterized. Phylogenetic analysis based on full 16S rRNA gene sequences revealed that the isolate is a member of the Gammaproteobacteria, forming an independent, deep phylogenetic lineage. It is most closely related to members of the genera Methylocaldum, Methylococcus and Natronocella, with sequence similarities below 91 %. Strain TUD-YJ37T was an obligately aerobic, ovoid, Gram-negative bacterium, motile by means of a polar flagellum. It utilized C2–C10 fatty acids as carbon and energy sources. The temperature range for growth was 20–35 °C, with an optimum of 30 °C; the pH range was 6.0–8.0, without a clear optimum. The major respiratory quinone was Q-8. Polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unidentified phospholipids, an unidentified aminolipid and another unidentified lipid. The predominant fatty acids in the membrane polar lipids were C16 : 1ω7c, C16 : 0 and C18 : 1ω7c. The G+C content of the genomic DNA was 67.4 mol%. On the basis of phenotypic, chemotaxonomic and molecular data, the isolate is proposed to represent a novel genus and species, for which the name Plasticicumulans acidivorans gen. nov., sp. nov. is proposed. The type strain of Plasticicumulans acidivorans is TUD-YJ37T ( = DSM 23606T  = CBS 122990T).

Utilization of arylaliphatic nitriles by haloalkaliphilic Halomonas nitrilicus sp. nov. isolated from soda soils

An enrichment culture from saline soda soils, using acetate as carbon and energy source and 2-phenylpropionitrile as nitrogen source (PPN) at pH 10, resulted in the isolation of strain ANL-αCH3. The strain was identified as a representative of the genus Halomonas in the Gammaproteobacteria. The bacterium was capable of PPN utilization as a nitrogen source only, while phenylacetonitrile (PAN) served both as carbon, energy and nitrogen source. This capacity was not described previously for any other haloalkaliphilic bacteria. Apart from the nitriles mentioned above, resting cells of ANL-αCH3 also hydrolyzed mandelonitrile, benzonitrile, acrylonitrile, and phenylglycinonitrile, presumably using nitrilase pathway. Neither nitrile hydratase nor amidase activity was detected. The isolate showed a capacity to grow with benzoate and salicylate as carbon and energy source and demonstrated the ability to completely mineralize PAN. These clearly indicated a potential to catabolize aromatic compounds. On the basis of unique phenotype and distinct phylogeny, strain ANL-αCH3 is proposed as a novel species of the genus Halomonas—Halomonas nitrilicus sp. nov.

List of new names and new combinations previously effectively, but not validly, published

The purpose of this announcement is to effect the valid publication of the following new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof, or an electronic copy of the published paper, to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries (i.e. documents certifying deposition and availability of type strains). It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below, and these authors' names will be included in the author index of the present issue and in the volume author index. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in bacteriological nomenclature. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.

Microbial isobutyronitrile utilization under haloalkaline conditions

The utilization of isobutyronitrile (iBN) as a C and N source under haloalkaline conditions by microbial communities from soda lake sediments and soda soils was studied. In both cases, a consortium consisting of two different bacterial species capable of the complete degradation and utilization of iBN at pH 10 was selected. The soda lake sediment consortium consisted of a new actinobacterium and a gammaproteobacterium from the genus Marinospirillum. The former was capable of fast hydrolysis of aliphatic nitriles to the corresponding amides and much-slower further hydrolysis of the amides to carboxylic acids. Its partner cannot hydrolyze nitriles but grew rapidly on amides and carboxylic acids, thus acting as a scavenger of products released by the actinobacterium. The soda soil consortium consisted of two Bacillus species (RNA group 1). One of them initiated nitrile hydrolysis, and the other utilized the hydrolysis products isobutyroamide (iBA) and isobutyrate (iB). In contrast to the actinobacterium, the nitrile-hydrolyzing soil Bacillus grew rapidly with hydrolysis products, but it was dependent on vitamins most probably supplied by its product-utilizing partner. All four bacterial strains isolated were moderately salt-tolerant alkaliphiles with a pH range for growth from pH 7.0 to 8.5 up to 10.3 to 10.5. However, both their nitrile hydratase and amidase activities had a near-neutral pH optimum, indicating an intracellular localization of these enzymes. Despite this fact, the study demonstrated a possibility of whole-cell biocatalytic hydrolysis of various nitriles at haloalkaline conditions.