Isolation of Thermus strains from hot composts (60 to 80 degrees C)

Responses of greenhouse gas emissions to aeration coupled with functional membrane during industrial-scale composting of dairy manure: Insights into bacterial community composition and function

Greenhouse gas (GHG) emissions from manure management processes deserve more attention. Using three industrial-scale experiments, this study comprehensively evaluated the effects of different aeration coupled with semi-permeable membrane-covered strategies on the structure and function of bacterial communities and their impact on GHG emissions during dairy manure aerobic composting. The succession of the bacterial communities tended to be consistent for similar aeration strategies. Ruminiclostridium and norank_f__MBA03 were significantly positively correlated with the methane emission rate, and forced aeration coupled with semi-permeable membrane-covered decreased GHG emissions by inhibiting these taxa. Metabolism was the most active function of the bacterial communities, and its relative abundance accounted for 75.69%-80.23%. The combined process also enhanced carbohydrate metabolism and amino acid metabolism. Therefore, forced aeration coupled with semi-permeable membrane-covered represented a novel strategy for reducing global warming potential by regulating the structure and function of the bacterial communities during aerobic composting of dairy manure.

Effect comparisons of different conditioners and microbial agents on the degradation of estrogens during dairy manure composting

To investigate the degradation efficiency of conditioners and commercial microbial agents on estrogens (E1, 17α-E2, 17β-E2, E3, EE2, and DES) in the composting process of dairy manure, seven different treatments (RHB-BF, OSP-BF, SD-BF, MR-BF, MR-FS, MR-EM, and MR-CK) under forced ventilation conditions were composted and monitored regularly for 30 days. The results indicated that the removal rates of estrogens in seven treatments ranged from 95.35% to 99.63%, meanwhile the degradation effect of the composting process on 17β-Estradiol equivalent (EEQ) was evaluated, and the removal rate of ΣEEQ ranged from 96.42% to 99.72%. With the combined addition of rice husk biochar (RHB) or oyster shell powder (OSP) and bio-bacterial fertilizer starter cultures (BF), namely RHB-BF and OSP-BF obviously promoted the rapid degradation of estrogens. 17β-E2 was completely degraded on the fifth day of composting in OSP-BF. Microbial agents have some promotional effect and enhances the microbial degradation of synthetic estrogen (EE2, DES). According to the results of RDA, pH and EC were the main environmental factors affecting on the composition and succession of estrogen-related degrading bacteria in composting system. As predominant estrogens-degrading genera, Acinetobacter, Bacillus, and Pseudomonas effected obviously on the change of estrogens contents. The research results provide a practical reference for effective composting of dairy manure to enhancing estrogens removal and decreasing ecological risk.

Thermophilic Fungi as the Microbial Agents of Choice for the Industrial Co-Fermentation of Wood Wastes and Nitrogen-Rich Organic Wastes to Bio-Methane

The novel industrial approach of co-fermenting wood wastes with agricultural wastes that are rich in nitrogen such as animal manures to produce bio-methane (renewable natural gas) fuel via thermophilic anaerobic digestion mimics an analogous process occurring in lower termites, but it relies instead on thermophilic fungi along with other thermophilic microorganisms comprising suitable bacteria and archaea. Wood microbial hydrolysis under thermophilic temperatures (range of 55 °C to 70 °C) and aerobic or micro-aerobic conditions constitutes the first step of the two-step (hydrolysis and fermentation) dry thermophilic anaerobic digestion industrial process, designated as "W2M3+2", that relies on thermophilic fungi species, most of which grow naturally in wood piles. Eleven thermophilic fungi have been identified as likely agents of the industrial process, and their known growth habitats and conditions have been reviewed. Future research is proposed such that the optimal growth temperature of these thermophilic fungi could be increased to the higher thermophilic range approaching 70 °C, and a tolerance to partial anaerobic conditions can be obtained by modifying the fungal microbiome via a symbiotic existence with bacteria and/or viruses.

Thermally enhanced biodegradation of benzo[a]pyrene and benzene co-contaminated soil: Bioavailability and generation of ROS

In this study, a set of comprehensive experiments were conducted to explore the effects of temperature on the biodegradation, bioavailability, and generation of reactive oxygen species (ROS) by thermally enhanced biodegradation (TEB) under benzene and BaP co-contaminated conditions. The biodegradation rates of benzene increased from 57.4% to 88.7% and 84.9%, and the biodegradation efficiency of BaP was enhanced from 15.8% to 34.6% and 28.6%, when the temperature was raised from the ambient temperature of 15 °C to 45 °C and 30 °C, respectively. In addition, the bioavailability analysis results demonstrated that the water- and butanol-extractable BaP increased with elevated temperatures. High enzymatic activities and PAH-RHD_α gene in gram-positive bacteria favored the long-term elevated temperatures (30 and 45 °C) compared to gram-negative bacteria. Moreover, ROS species (O₂^•- and •OH) generation was detected which were scavenged by the increased superoxide dismutase and catalase activities at elevated temperatures. Soil properties (pH, TOC, moisture, total iron, Fe³⁺, and Fe²⁺) were affected by the temperature treatments, revealing that metal-organic-associated reactions occurred during the TEB of benzene-BaP co-contamination. The results concluded that biodegradation of benzene-BaP co-contamination was greatly improved at 45 °C and that microbial activities enhanced the biodegradation under TEB via the increased bioavailability and generation and degradation of ROS.

Investigation of potential inhibitor properties of violacein against HIV-1 RT and CoV-2 Spike RBD:ACE-2

A violacein-producing bacterium was isolated from a mud sample collected near a hot spring on Kümbet Plateau in Giresun Province and named the GK strain. According to the phylogenetic tree constructed using 16S rRNA gene sequence analysis, the GK strain was identified and named Janthinobacterium sp. GK. The crude violacein pigments were separated into three different bands on a TLC sheet. Then violacein and deoxyviolacein were purified by vacuum liquid column chromatography and identified by NMR spectroscopy. According to the inhibition studies, the HIV-1 RT inhibition rate of 1 mM violacein from the GK strain was 94.28% and the CoV-2 spike RBD:ACE2 inhibition rate of 2 mM violacein was 53%. In silico studies were conducted to investigate the possible interactions between violacein and deoxyviolacein and three reference molecules with the target proteins: angiotensin-converting enzyme 2 (ACE2), HIV-1 reverse transcriptase, and SARS-CoV-2 spike receptor binding domain. Ligand violacein binds strongly to the receptor ACE2, HIV-1 reverse transcriptase, and SARS-CoV-2 spike receptor binding domain with a binding energy of −9.94 kcal/mol, −9.32 kcal/mol, and −8.27 kcal/mol, respectively. Deoxyviolacein strongly binds to the ACE2, HIV-1 reverse transcriptase, and SARS-CoV-2 spike receptor binding domain with a binding energy of −10.38 kcal/mol, -9.50 kcal/mol, and −8.06 kcal/mol, respectively. According to these data, violacein and deoxyviolacein bind to all the receptors quite effectively. SARS-CoV-2 spike protein and HIV-1-RT inhibition studies with violacein and deoxyviolacein were performed for the first time in the literature.

Lytic polysaccharide monooxygenases (LPMOs) producing microbes: A novel approach for rapid recycling of agricultural wastes

Out of the huge quantity of agricultural wastes produced globally, rice straw is one of the most abundant ligno-cellulosic waste. For efficient utilization of these wastes, several cost-effective biological processes are available. The practice of field level in-situ or ex-situ decomposition of rice straw is having less degree of adoption due to its poor decomposition ability within a short time span between rice harvest and sowing of the next crop. Agricultural wastes including rice straw are in general utilized by using lignocellulose degrading microbes for industrial metabolite or compost production. However, bioconversion of crystalline cellulose and lignin present in the waste, into simple molecules is a challenging task. To resolve this issue, researchers have identified a novel new generation microbial enzyme i.e., lytic polysaccharide monooxygenases (LPMOs) and reported that the combination of LPMOs with other glycolytic enzymes are found efficient. This review explains the progress made in LPMOs and their role in lignocellulose bioconversion and the possibility of exploring LPMOs producers for rapid decomposition of agricultural wastes. Also, it provides insights to identify the knowledge gaps in improving the potential of the existing ligno-cellulolytic microbial consortium for efficient utilization of agricultural wastes at industrial and field levels.

Complete Genome Resequencing of Thermus thermophilus Strain TMY by Hybrid Assembly of Long- and Short-Read Sequencing Technologies

Complete genome resequencing was conducted for Thermus thermophilus strain TMY by hybrid assembly of Oxford Nanopore Technologies long-read and MGI short-read data. Errors in the previously reported genome sequence determined by PacBio technology alone were corrected, allowing for high-quality comparative genomic analysis of closely related T. thermophilus genomes.

Co-composting of cotton residues with olive mill wastewater: process monitoring and evaluation of the diversity of culturable microbial populations

With the aim to recommend an integrated alternative for the combined treatment of olive mill wastewater (OMW) and cotton residues (CR), and the production of high value and environmentally friendly products, two compost piles were set up. The first pile (control, pile 1) consisted of ginned CR, whereas the second (pile 2) was made of CR with the addition of OMW. A series of physicochemical parameters and the culturable microbial diversity in both piles were assessed. Co-composting (pile 2) displayed higher temperatures during the whole process, a prolonged second thermophilic phase and temperature values higher than 40 °C even after the thermophilic stage. Comparing the physicochemical parameters of the pile 2 with those of the pile 1, it was deduced that pH in the former was more acidic during the onset of the process; the EC values were higher throughout the process, while the levels of ammonium and nitrate nitrogen, as well as the NH₄⁺/NO₃^- ratios, were lower at most of the sampling dates. By evaluating the abovementioned results, it was estimated that the co-composting process headed sooner toward stability and maturity, Isolated microorganisms from both piles were identified as members of the genera Brevibacillus, Serratia, Klebsiella, and Aspergillus, whereas active thermotolerant diazotrophs were detected in both piles at the 2nd thermophilic phase emerging a promising prospect upon further evaluation for enhancing the end-product quality. Our findings indicate that co-composting is an interesting approach for the exploitation of large quantities of agro-industrial residues with a final product suitable for improving soil fertility and health.

Effects of humic acid modified oyster shell addition on lignocellulose degradation and nitrogen transformation during digestate composting

The aim of this work was to investigate the performance of a novel humic acid modified oyster shell (MOS) bulking agent on the digestate composting. MOS was prepared by immobilizing humic acid onto oyster shell using solid phase grafting method, and then applied to the composting process. Results showed more obvious degradation of lignocellulose was observed in the MOS treatment, which was probably due to the high relative abundance of Actinobacteria. Moreover, the addition of MOS could significantly preserve NH₄⁺ and reduce the NO₃^- generation with the decreasing abundance of ammonia-oxidizing bacteria and archaea. Besides, adding MOS reduced the N₂O emission by 59.63% compared with the control. After composting, excitation-emission matrix fluorescence spectra demonstrated that the humification degree as well as compost maturity was enhanced with MOS added.

Molecular analyses of the diversity and function of the family 1 β-glucosidase-producing microbial community in compost

The diversity and transcription efficiency of GH1 family β-glucosidase genes were investigated in natural and inoculated composts using a DNA clone library and real-time qPCR. Compositional differences were observed in the functional community between both composting processes. Proteobacteria, Actinobacteria, Firmicutes, and Chloroflexi were the dominant phyla. Twenty representative β-glucosidase genes were quantitatively analyzed from DNA and RNA pools. Principal component analysis and Pearson's correlation analysis showed that cellulose degradation is correlated with the composition and succession of functional microbial communities, and this correlation was mainly observed in Proteobacteria and Actinobacteria. Compared with inoculated compost, the functional microbial communities in natural compost with a low diversity index exhibited weak buffering capacity for function in response to environmental changes. This may explain the consistency and dysfunction of cellulose degradation and transcriptional regulation by dominant β-glucosidase genes. Except for the β-glucosidase genes encoding constitutive enzymes, individual β-glucosidase genes responded to environmental changes more drastically than the group β-glucosidase genes. Correlation results suggested that β-glucosidase genes belonging to Micrococcales played an important role in the regulation of intracellular β-glucosidase. These results indicated that the responses of functional microorganisms were different during both composting processes, and were reflected at both the individual and group levels.

Bio-process performance, evaluation of enzyme and non-enzyme mediated composting of vegetable market complex waste

Vegetable Market have become major sources of organic waste. Some of such waste when being diverted to landfills not only increase the landfill loading but also contribute to increase greenhouse gas emission. Of the many technologies available in handling such hugely generated waste, composting has proven very effective for decades. Enzyme and non-enzyme mediated aerobic composting of vegetable market complex waste (VMCW) have been investigated. Conventional composting technique though being capable of handling large quantum of waste are found to consume more time. Proven to be disadvantages factor. In the present investigation, the pre-cultured seed inoculums used for vegetable market complex waste, shortened the typical composting period from 45 to 9 days for the first time. Also, rapid size and volume reduction of VMCW was witnessed. The organic degradation of VMCW was observed as 42% (82 ± 2.83% to 40.82 ± 0.61%), with a volume reduction from 0.012m³ to 0.003 m³ within 9 days. An enriched nutrients NPK level of compost bio-fertilizer was recorded as 0.91% w/w, 0.5% w/w and 1.029% w/w respectively. Compost maturity observed through the X-ray diffraction (XRD) analysis of the manure confirmed the conversion of the crystal structure of the compost particle to amorphous form and the mineralization of organic matter during the composting. Thus, the fermented pre-cultured seed inoculums favored an enhanced nutrients level with shortened composting time.

Characterization of a novel carboxylesterase belonging to family VIII hydrolyzing β-lactam antibiotics from a compost metagenomic library

A novel esterase, EstCS3, was isolated from a metagenomic library constructed from a compost. The EstCS3, which consists of 409 amino acids with an anticipated molecular mass of 44 kDa, showed high amino acid sequence identities to predicted esterases, serine hydrolases and β-lactamases from uncultured and cultured bacteria. Phylogenetic analysis suggested that EstCS3 belongs to family VIII of lipolytic enzymes. EstCS3 had catalytic Ser78 residue in the consensus tetrapeptide motif SXXK, which is characteristic of family VIII esterases. Two conserved YXX and W(H or K)XG motifs in an oxyanion hole of family VIII esterases were also present in EstCS3. EstCS3 demonstrated the highest activity toward p-nitrophenyl butyrate (C4) and was stable up to 70 °C with optimal activity at 55 °C. EstCS3 had optimal activity at pH 8 and maintained its stability within pH range of 7-10. EstCS3 had over 70% activity in the presence of 20% (v/v) methanol and DMSO and hydrolyzed sterically hindered tertiary alcohol esters of t-butyl acetate and linalyl acetate. EstCS3 hydrolyzed ampicillin, cephalothin and cefepime. The properties of EstCS3, including moderate thermostability, stability against organic solvents and activity toward esters of tertiary alcohols, indicated that it has the potential to be used in industrial applications.

Addition of oyster shell to enhance organic matter degradation and nitrogen conservation during anaerobic digestate composting

Anaerobic digested residue (DR) is the main by-product from biogas plants, and it is predominantly used as organic fertilizer after composting. To resolve the problems of long duration and nitrogen loss in conventional composting, bulking agents are always added during the composting process. In this study, oyster shell (OS) was used as a bulking agent for DR composting. Four treatments were conducted by mixing DR and OS at different concentrations (0%, 10%, 20% and 30%, based on wet weight) and then composting the mixtures for 40 days. The results showed that the organic matter (OM) degradation efficiency was enhanced by 5.62%, 12.15% and 16.98% with increasing amounts of OS addition. The increased content of microbial biomass carbon in the compost indicated a suitable living environment for aerobic microbes with added OS, which could explain the increased OM degradation efficiency. Compared with the control, the NH3 emissions in the treatments with 10%, 20% and 30% OS were decreased by 13.81%, 33.33% and 53.76%, respectively. The increase in total nitrogen content in the compost is probably due to the absorption of NH3 by OS. Results indicated that OS is a suitable bulking agent for DR composting and that the addition of 20-30% OS can significantly enhance composting performance.

Food waste composting - Is it really so simple as stated in scientific literature? - A case study

Food waste has recently gained much worldwide interest due to its influence on the environment, economy and society. Gathering and recycling of food waste is the essential issue in the waste management and the interest in processing food waste arises mainly out of influence of the processes of food putrefaction on the environment. Composting of food waste encounters a number of technical challenges, arising weak physical structure of food waste with weak porosity, high content of water, low carbon-to-nitrogen relation and fast hydrolysis and accumulation of organic acids during composting. Therefore, the aim of this study was to investigate the challenges facing installations intended for food waste composting, with the purpose to their optimization with use of appropriate additives. Physico-chemical, biochemical characteristics and phytotoxicity of the produced compost has been measured. Two additives (20% biochar and 20% sawdust) were chosen from experimental variants I-XII containing different additives (biochar, Devonian sand, sawdust) in diverse concentration. The use of selected additives seems to slightly increase potential of hydrogen value and carbon-to-nitrogen ratio, while decreasing electrical conductivity in comparison with control sample. The results obtained also show that the addition of biochar leads to an increase dehydrogenase, phosphatase and arylsulphatase activities and addition of sawdust has a positive effect on beta-D-glucosidase, protease, phosphatase and arylsulphatase activities. The phytotoxicity test shows that the compost made of food waste (control sample) and with addition of biochar is toxic to plants. By contrast, the addition of sawdust shows that the compost was not phytotoxic. In conclusion, the addition of additives does not provide unambiguous results in terms of the quality of the final product in all monitored parameters. Therefore, we can state that food waste was reduced and hygienized, and that the final product does not meet conditions for mature compost.

Characterization of a Novel Moderately Thermophilic Solvent-Tolerant Esterase Isolated From a Compost Metagenome Library

A novel esterase, EstCS1, was isolated from a compost metagenomics library. The EstCS1 protein, which consists of 309 amino acid residues with an anticipated molecular mass of 34 kDa, showed high amino acid sequence identities to predicted esterases and alpha/beta hydrolases (59%) from some cultured bacteria and to predicted lipases/esterases from uncultured bacteria. The phylogenetic analysis suggested that the EstCS1 belongs to the hormone-sensitive lipase family of lipolytic enzyme classification and contains a catalytic triad including Ser155–Asp255–His285. The Ser155 residue of the catalytic triad in the EstCS1 was located in the consensus active-site motif, GXSXG. Besides, a conserved HGGG motif placed in an oxyanion hole of the hormone-sensitive lipase family was discovered, too. The EstCS1 demonstrated the highest activity toward p-nitrophenyl propionate (C3) and caproate (C6) and was normally stable up to 60°C with optimal activity at 50°C. In addition, an optimal activity was observed at pH 8, and the EstCS1 possessed its stability within the pH range between 5 and 10. Interestingly, EstCS1 had an outstanding stability in up to 30% (v/v) organic solvents and activity over 50% in the presence of 50% (v/v) acetone, ethanol, dimethyl sulfoxide (DMSO), and N,N-dimethylformamide. The EstCS1 hydrolyzed sterically hindered tertiary alcohol esters of t-butyl acetate and linalyl acetate. Considering the properties, such as the moderate thermostability, stability against organic solvents, and activity toward esters of tertiary alcohols, the EstCS1 will be worthwhile to be used for organic synthesis and related industrial applications.

Characterization and biotechnological application of protease from thermophilic Thermomonas haemolytica

In this study, it was aimed to determine the ability to produce protease enzyme of Thermomonas haemolytica isolated from geothermal Nenehatun hot spring in Turkey and utilization of this enzyme in the detergent industry to remove protein stains. The protease-producing strains were screened from hot springs, and a potential strain was identified as T. haemolytica according to morphological, physiological and biochemical characteristics and sequence of 16S rRNA gene. Maximum protease activity was observed at 55 °C and pH 9.0 at 72 h of incubation. Activity was very stable between 50 and 65 °C and pH 8.0-10.0, respectively. The enzyme activity was significantly inhibited by PMSF and partly inhibited by EDTA, EGTA, SDS, and urea. Some divalent metal ions such as Ca²⁺, Mg²⁺, and Mn²⁺ increased the enzyme activity, while Zn²⁺ and Cu²⁺ decreased. Michaelis-Menten constant (K_m) and maximum velocity (V_max) values were calculated by Lineweaver-Burk plot as 125 EU/ml and 1262 mg/ml, respectively. The biochemical characterization of the protease obtained from T. haemolytica was performed and applied on the blood and grass-stained fabrics with detergent to evaluate the stain removal performance of the enzyme. It was observed that the application of detergent with enzyme was more effective than the detergent without enzyme to clean up the stained fabrics. This is the first report of characterization of the protease of T. haemolytica. According to results obtained from this study, this new strain is a promising candidate for industrial applications in production of detergent.

The changes in carbon, nitrogen components and humic substances during organic-inorganic aerobic co-composting

In this article, the changes in carbon, nitrogen components, and humic substances during organic-inorganic aerobic co-composting, with adding biochar as an additive or not, were studied. Results showed that adding a certain amount of inorganic fertilizers had no adverse effects on the compost fermentation process. Biochar enhanced the temperature, pH, oxygen content in the compost piles and ultimately hastened the fermentation process. Biochar contributed to the decomposition of hemicellulose, cellulose, lignin and promoted compost humification. Adding biochar increased the contents of acid hydrolysis nitrogen, amino acid nitrogen, amino sugar nitrogen, unidentified organic nitrogen and decreased the content of ammonia organic nitrogen thus improved nitrogen transformation and reduced nitrogen loss. The addition of biochar increased the nutrients contents in mature composts. The amendment of 10-15% biochar by weight as an additive would be optimum for the co-composting of organic-inorganic materials. These results contributed to produce value-added composting fertilizers.

Biogeography of thermophiles and predominance of Thermus scotoductus in domestic water heaters

Built systems such as water heaters can harbor extremophiles similar to those residing in natural hot springs, but the extent of colonization is not well understood. To address this, we conducted a survey of thermophilic microorganisms in household water heaters across the United States. Filter samples and inoculated cultures were collected by citizen-scientists from 101 homes. Draft genomes were assembled from cultured isolates and 16S rRNA genes were sequenced from filter samples. 28% of households harbored communities with unambiguous DNA signatures of thermophilic organisms, 36% of households provided viable inocula, and 21% of households had both. All of the recovered cultures as well as the community sequencing results revealed Thermus scotoductus to be the dominant thermophile in domestic water heaters, with a minority of water heaters also containing Meiothermus species and a few containing Aquificae. Sequence distance comparisons show that allopatric speciation does not appear to be a strong control on T. scotoductus distribution. Our results demonstrate that thermophilic organisms are widespread in hot tap water, and that Thermus scotoductus preferentially colonizes water heaters at the expense of local environmental Thermus strains.

The structural and functional contributions of β-glucosidase-producing microbial communities to cellulose degradation in composting

BACKGROUND

Compost habitats sustain a vast ensemble of microbes that engender the degradation of cellulose, which is an important part of global carbon cycle. β-Glucosidase is the rate-limiting enzyme of degradation of cellulose. Thus, analysis of regulation of β-glucosidase gene expression in composting is beneficial to a better understanding of cellulose degradation mechanism. Genetic diversity and expression of β-glucosidase-producing microbial communities, and relationships of cellulose degradation, metabolic products and the relative enzyme activity during natural composting and inoculated composting were evaluated.

RESULTS

Compared with natural composting, adding inoculation agent effectively improved the degradation of cellulose, and maintained high level of the carboxymethyl cellulose (CMCase) and β-glucosidase activities in thermophilic phase. Gene expression analysis showed that glycoside hydrolase family 1 (GH1) family of β-glucosidase genes contributed more to β-glucosidase activity in the later thermophilic phase in inoculated compost. In the cooling phase of natural compost, glycoside hydrolase family 3 (GH3) family of β-glucosidase genes contributed more to β-glucosidase activity. Intracellular β-glucosidase activity played a crucial role in the regulation of β-glucosidase gene expression, and upregulation or downregulation was also determined by extracellular concentration of glucose. At sufficiently high glucose concentrations, the functional microbial community in compost was altered, which may contribute to maintaining β-glucosidase activity despite the high glucose content.

CONCLUSION

This research provides an ecological functional map of microorganisms involved in carbon metabolism in cattle manure-rice straw composting. The performance of the functional microbial groups in the two composting treatments is different, which is related to the cellulase activity and cellulose degradation, respectively.

Compost supplementation with nutrients and microorganisms in composting process

The composting is an aerobic, microorganism-mediated, solid-state fermentation process by which different organic materials are transformed into more stable compounds. The product obtained is the compost, which contributes to the improvement of physical, chemical and microbiological properties of the soil. However, the compost usage in agriculture is constrained because of its long-time action and reduced supply of nutrients to the crops. To enhance the content of nutrients assimilable by the plants in the compost, its supplementation with nutrients and inoculation with microorganisms have been proposed. The objective of this work was to review the state of the art on compost supplementation with nutrients and the role played by the microorganisms involved (or added) in their transformation during the composting process. The phases of composting are briefly compiled and different strategies for supplementation are analyzed. The utilization of nitrogenous materials and addition of microorganisms fixing nitrogen from the atmosphere or oxidizing ammonia into more assimilable for plants nitrogenous forms are analyzed. Several strategies for nitrogen conservation during composting are presented as well. The supplementation with phosphorus and utilization of microorganisms solubilizing phosphorus and potassium are also discussed. Main groups of microorganisms relevant during the composting process are described as well as most important strategies to identify them. In general, the development of this type of nutrient-enriched bio-inputs requires research and development not only in the supplementation of compost itself, but also in the isolation and identification of microorganisms and genes allowing the degradation and conversion of nitrogenous substances and materials containing potassium and phosphorus present in the feedstocks undergoing the composting process. In this sense, most important research trends and strategies to increase nutrient content in the compost are provided in this work.

Cupriavidus necator H16 Uses Flavocytochrome c Sulfide Dehydrogenase To Oxidize Self-Produced and Added Sulfide

Production of sulfide (H₂S, HS^-, and S^2-) by heterotrophic bacteria during aerobic growth is a common phenomenon. Some bacteria with sulfide:quinone oxidoreductase (SQR) and persulfide dioxygenase (PDO) can oxidize self-produced sulfide to sulfite and thiosulfate, but other bacteria without these enzymes release sulfide into the medium, from which H₂S can volatilize into the gas phase. Here, we report that Cupriavidus necator H16, with the fccA and fccB genes encoding flavocytochrome c sulfide dehydrogenases (FCSDs), also oxidized self-produced H₂S. A mutant in which fccA and fccB were deleted accumulated and released H₂S. When fccA and fccB were expressed in Pseudomonas aeruginosa strain Pa3K with deletions of its sqr and pdo genes, the recombinant rapidly oxidized sulfide to sulfane sulfur. When PDO was also cloned into the recombinant, the recombinant with both FCSD and PDO oxidized sulfide to sulfite and thiosulfate. Thus, the proposed pathway is similar to the pathway catalyzed by SQR and PDO, in which FCSD oxidizes sulfide to polysulfide, polysulfide spontaneously reacts with reduced glutathione (GSH) to produce glutathione persulfide (GSSH), and PDO oxidizes GSSH to sulfite, which chemically reacts with polysulfide to produce thiosulfate. About 20.6% of sequenced bacterial genomes contain SQR, and only 3.9% contain FCSD. This is not a surprise, since SQR is more efficient in conserving energy because it passes electrons from sulfide oxidation into the electron transport chain at the quinone level, while FCSD passes electrons to cytochrome c The transport of electrons from the latter to O₂ conserves less energy. FCSDs are grouped into three subgroups, well conserved at the taxonomic level. Thus, our data show the diversity in sulfide oxidation by heterotrophic bacteria.IMPORTANCE Heterotrophic bacteria with SQR and PDO can oxidize self-produced sulfide and do not release H₂S into the gas phase. C. necator H16 has FCSD but not SQR, and it does not release H₂S. We confirmed that the bacterium used FCSD for the oxidation of self-produced sulfide. The bacterium also oxidized added sulfide. The common presence of SQRs, FCSDs, and PDOs in heterotrophic bacteria suggests the significant role of heterotrophic bacteria in sulfide oxidation, participating in sulfur biogeochemical cycling. Further, FCSDs have been identified in anaerobic photosynthetic bacteria and chemolithotrophic bacteria, but their physiological roles are unknown. We showed that heterotrophic bacteria use FCSDs to oxidize self-produced sulfide and extraneous sulfide, and they may be used for H₂S bioremediation.

Fungal and bacterial successions in the process of co-composting of organic wastes as revealed by 454 pyrosequencing

Composting is viewed as one of the primary methods to treat organic wastes. Co-composting may improve the efficiency of this treatment by establishing the most suitable conditions for decomposers than those present in the individual wastes. Given that bacteria and fungi are the driving agents of composting, information about the composition of their communities and dynamics during composting may improve reproducibility, performance and quality of the final compost as well as help to evaluate the potential human health risk and the choice of the most appropriate application procedure. In this study, the co-composting of mixtures containing two similar components (organic fraction of municipal solid waste and sawdust polluted by oil) and one discriminate component (sewage sludges of different origin) were investigated. Bacterial and fungal community successions in the two mixtures were analyzed during the composting process by determining the change in their structural dynamics using qPCR and 454 pyrosequencing methods in a lab experiment for a period of 270 days. During the initial composting stage, the number of 16S bacterial copies was (3.0±0.2) x 10⁶ and (0.4±0.0) x 10⁷ g^-1, and the Rhodospiralles and Lactobacialles orders dominated. Fungal communities had (2.9±0.0) x10⁵ and (6.1±0.2) x10⁵ ITS copies g^-1, and the Saccharomycetales order dominated. At the end of the thermophilic stage on the 30^th day of composting, bacterial and fungal communities underwent significant changes: dominants changed and their relative abundance decreased. Typical compost residents included Flavobacteriales, Chitinophagaceae and Bacterioidetes for bacteria and Microascaceae, Dothideomycetes, Eurotiomycetes, Sordariomycetes, and Agaricomycetes for fungi. During the later composting stages, the dominating taxa of both bacterial and fungal communities remained, while their relative abundance decreased. In accordance with the change in the dominating OTUs, it was concluded that the dynamics of the bacterial and fungal communities were not similar. Analysis by non-metric multidimensional scaling (NMDS) revealed that the bacterial communities of the two composts became progressively more similar; a similar trend was followed by the fungal community.

The distribution of active β-glucosidase-producing microbial communities in composting

The composting ecosystem is a suitable source for the discovery of novel microorganisms and secondary metabolites. Cellulose degradation is an important part of the global carbon cycle, and β-glucosidases complete the final step of cellulose hydrolysis by converting cellobiose to glucose. This work analyzes the succession of β-glucosidase-producing microbial communities that persist throughout cattle manure - rice straw composting, and evaluates their metabolic activities and community advantage during the various phases of composting. Fungal and bacterial β-glucosidase genes belonging to glycoside hydrolase families 1 and 3 (GH1 and GH3) amplified from DNA were classified and gene abundance levels were analyzed. The major reservoirs of β-glucosidase genes were the fungal phylum Ascomycota and the bacterial phyla Firmicutes, Actinobacteria, Proteobacteria, and Deinococcus-Thermus. This indicates that a diverse microbial community utilizes cellobiose. The succession of dominant bacteria was also detected during composting. Firmicutes was the dominant bacteria in the thermophilic phase of composting; there was a shift to Actinomycetes in the maturing stage. Proteobacteria accounted for the highest proportions during the heating and thermophilic phases of composting. By contrast, the fungal phylum Ascomycota was a minor microbial community constituent in thermophilic phase of composting. Combined with the analysis of the temperature, cellulose degradation rate and the carboxymethyl cellulase and β-glucosidase activities showed that the bacterial GH1 family β-glucosidase genes make greater contribution in cellulose degradation at the later thermophilic stage of composting. In summary, even GH1 bacteria families β-glucosidase genes showing low abundance in DNA may be functionally important in the later thermophilic phase of composting. The results indicate that a complex community of bacteria and fungi expresses β-glucosidases in compost. Several β-glucosidase-producing bacteria and fungi identified in this study may represent potential indicators of composting in cellulose degradation.

Streptomyces ovatisporus sp. nov., isolated from deep marine sediment

The taxonomic position of a Gram-staining-positive strain, designated strain S4702T was isolated from a marine sediment collected from the southern Black Sea coast, Turkey, determined using a polyphasic approach. The isolate was found to have chemotaxonomic, morphological and phylogenetic properties consistent with its classification as representing a member of the genus Streptomyces and formed a distinct phyletic line in the 16S rRNA gene tree. S4702T was found to be most closely related to the type strains of Streptomyces marinus(DSM 41968T; 97.8 % sequence similarity) and Streptomyces abyssalis (YIM M 10400T; 97.6 %). 16S rRNA gene sequence similarities with other members of the genus Streptomyces were lower than 97.5 %. DNA-DNA relatedness of S4702T and the most closely related strain S. marinus DSM 41968T was 21.0 %. The G+C content of the genomic DNA was 72.5 mol%. The cell wall of the strain contained l,l-diaminopimelic acid and the cell-wall sugars were glucose and ribose. The major cellular fatty acids were identified as anteiso-C15 : 0, iso-C16 : 0, anteiso-C17 : 0 and iso-C15 : 0. The predominant menaquinone was MK-9(H8). The polar lipid profile of S4702T consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannoside. S4702T could be distinguished from its closest phylogenetic neighbours using a combination of chemotaxonomic, morphological and physiological properties. Consequently, it is proposed that S4702T represents a novel species of the genus Streptomyces, for which the name Streptomyces ovatisporus sp. nov. is proposed. The type strain is S4702T (DSM 42103T=KCTC 29206T=CGMCC 4.7357T).

Generation of acid mine drainage around the Karaerik copper mine (Espiye, Giresun, NE Turkey): implications from the bacterial population in the Acısu effluent

The Karaerik Cu mine is a worked-out deposit with large volumes of tailings and slags which were left around the mine site without any protection. Natural feeding of these material and run-off water from the mineralised zones into the Acısu effluent causes a serious environmental degradation and creation of acid mine drainage (AMD) along its entire length. This research aims at modelling the formation of AMD with a specific attempt on the characterisation of the bacterial population in association with AMD and their role on its occurrence. Based on 16SrRNA analyses of the clones obtained from a composite water sample, the bacterial community was determined to consist of Acidithiobacillus ferrivorans, Ferrovum myxofaciens, Leptospirillum ferrooxidans and Acidithiobacillus ferrooxidans as iron-oxidising bacteria, Acidocella facilis, Acidocella aluminiidurans, Acidiphilium cryptum and Acidiphilium multivorum as iron-reducing bacteria, and Acidithiobacillus ferrivorans, Acidithiobacillus ferrooxidans, Acidithiobacillus thiooxidans and Acidiphilium cryptum as sulphur-oxidising bacteria. This association of bacteria with varying roles was interpreted as evidence of a concomitant occurrence of sulphur and iron cycles during the generation of AMD along the Acısu effluent draining the Karaerik mine.

Co-utilization of glucose and xylose by evolved Thermus thermophilus LC113 strain elucidated by (13)C metabolic flux analysis and whole genome sequencing

We evolved Thermus thermophilus to efficiently co-utilize glucose and xylose, the two most abundant sugars in lignocellulosic biomass, at high temperatures without carbon catabolite repression. To generate the strain, T. thermophilus HB8 was first evolved on glucose to improve its growth characteristics, followed by evolution on xylose. The resulting strain, T. thermophilus LC113, was characterized in growth studies, by whole genome sequencing, and (13)C-metabolic flux analysis ((13)C-MFA) with [1,6-(13)C]glucose, [5-(13)C]xylose, and [1,6-(13)C]glucose+[5-(13)C]xylose as isotopic tracers. Compared to the starting strain, the evolved strain had an increased growth rate (~2-fold), increased biomass yield, increased tolerance to high temperatures up to 90°C, and gained the ability to grow on xylose in minimal medium. At the optimal growth temperature of 81°C, the maximum growth rate on glucose and xylose was 0.44 and 0.46h(-1), respectively. In medium containing glucose and xylose the strain efficiently co-utilized the two sugars. (13)C-MFA results provided insights into the metabolism of T. thermophilus LC113 that allows efficient co-utilization of glucose and xylose. Specifically, (13)C-MFA revealed that metabolic fluxes in the upper part of metabolism adjust flexibly to sugar availability, while fluxes in the lower part of metabolism remain relatively constant. Whole genome sequence analysis revealed two large structural changes that can help explain the physiology of the evolved strain: a duplication of a chromosome region that contains many sugar transporters, and a 5x multiplication of a region on the pVV8 plasmid that contains xylose isomerase and xylulokinase genes, the first two enzymes of xylose catabolism. Taken together, (13)C-MFA and genome sequence analysis provided complementary insights into the physiology of the evolved strain.

Fontibacillus pullulanilyticus sp.nov. isolated from soil

Gram stain-negative, motile, catalase-, and oxidase- positive strain, designated DSHK107(T) was isolated from soil of Cukurova University campus in Adana, Turkey. Its taxonomy was investigated using a polyphasic approach. The strain grew at 20-42 °C (optimum, 30 °C), at pH 6.0-9.0 (optimum, pH 7.0) and in 0-2.0% NaCl (w/v). 16S rRNA gene sequence analysis revealed that the strain belonged to the genus Fontibacillus; strain DSHK107(T) showed highest sequence similarity to type strains Fontibacillus aquaticus GPTSA 19(T) (97.8%) and Fontibacillus panacisegetis P11-6(T) (97.0%). The major fatty acid of strain DSHK107(T) was anteiso-C15:0 (46.7). The polar lipids of strain DSHK107(T) consisted of dihosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, four unknown phospholipids, four unknown lipids, three unknown glycolipids, two unknown aminophospholipids, an unknown aminolipid, and an unknown aminophosphoglycolipid. The major isoprenoid quinone was MK-7. The DNA G+C content of DSHK107(T) was 42.1 mol%. DNA-DNA hybridization showed that the strain DSHK107(T) shared low DNA-DNA relatedness with F. aquaticus DSM 17643(T) , Fontibacillus solani A4STRO4(T) , and F. panacisegetis DSM 28129(T) (47, 58, and 59.3%, respectively). Thus, our results support the placement of strain DSHK107(T) within a separate and previously unrecognized species. On the basis of a taxonomic study using a polyphasic approach, strain DSHK107(T) is considered to represent a novel species of the genus Fontibacillus, for which the name Fontibacillus pullulanilyticus sp. nov. is proposed. The type strain is DSHK107(T) (=NCCB 100560(T)  = DSM 100116(T) ).

Brevibacillus gelatini sp. nov., isolated from a hot spring

Two Gram-stain-positive, moderately thermophilic, endospore-forming, rod-shaped, motile bacteria designated PDF4^T and PDF10, were isolated from Camkoy hot spring in the provinces of Aydın, Turkey and were characterized in order to determine their phylogenetic position. 16S rRNA gene sequence analysis revealed that the two strains belonged to the genus Brevibacillus. Strain PDF4^T showed highest 16S rRNA gene sequence similarity to strain PDF10 (99.5 %), Brevibacillus brevis DSM 30^T (98.9 %), Brevibacillus parabrevis DSM 8376^T (98.6 %) and Brevibacillus formosus DSM 9885^T (98.5 %); similarities to other species of the genus Brevibacillus were less than 98.5 %. The predominant fatty acids of strain PDF4^T were anteiso-C_15 : 0 (60.0 %) and iso-C_15 : 0 (22.3 %). The polar lipids of strain PDF4^T consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, an unknown phospholipid, two unknown lipid, an unknown aminophospholipid and two unknown aminolipids. MK-7 was detected as a sole respiratory quinone, and the cell wall of strain PDF4^T contained meso-diaminopimelic acid. The DNA G+C content of strain PDF4^T was 51.7 mol%. DNA-DNA hybridization showed less than 60 % relatedness between strain PDF4^T and type strains of the most closely related species given above. Based on these data, the two strains are considered to represent a novel species of the genus Brevibacillus, for which the name Brevibacillus gelatini sp. nov. is proposed. The type strain is PDF4^T ( = NCCB 100559^T = DSM 100115^T).

Thermus anatoliensis sp. nov., a thermophilic bacterium from geothermal waters of Buharkent, Turkey

A Gram-stain-negative, lack of motility, catalase- and oxidase- positive bacterium (strain MT1(T)) was isolated from Buharkent hot spring in Aydin, Turkey. Its taxonomy was investigated using a polyphasic approach. The strain was able to grow at 45-80 °C, pH 5.5-10.5 and with a NaCI tolerance up to 2.0% (w/v). Strain MT1(T) was able to utilize d-mannitol and l-arabinose, not able to utilize d-cellobiose as sole carbon source. 16S rRNA gene sequence analysis revealed that the strain belonged to the genus Thermus; strain MT1(T) detected low-level similarities of 16S rRNA gene sequences (below 97%) compared with all other species in this genus. The predominant fatty acids of strain MT1(T) were iso-C(15:0) (43.0%) and iso-C(17:0) (27.4%). Polar lipid analysis revealed a major phospholipid, one major glycolipid, one major aminophospholipid, two minor aminolipids, one minor phospholipid, and several minor glycolipids. The major isoprenoid quinone was MK-8. The DNA G+C content of MT1(T) was 69.6 mol%. On the basis of a taxonomic study using a polyphasic approach, strain MT1(T) is considered to represent a novel species of the genus Thermus, for which the name Thermus anatoliensis sp. nov. is proposed. The type strain is MT1(T) (=NCCB 100425(T) =LMG 26880(T)).

Purification and characterization of [Formula: see text]-mannanase from Bacillus pumilus (M27) and its applications in some fruit juices

Thermo alkaline mannanase was purified from the bacteria of Bacillus pumilus (M27) using the techniques of ammonium sulphate precipitation, DEAE-Sephadex ion exchange chromatography and Sephacryl S200 gel filtration chromatography with 111-fold and 36 % yield. It was determined that the enzyme had 2 sub-units including 35 kDa and 55 kDa in gel filtration chromatography and SDS-PAGE electrophoresis systems. The optimum pH and temperature was determined as 8 and 60 °C, respectively. It was also noticed that the enzyme did not lose its activity at a wide interval such as pH 3-11 and at high temperatures such as 90 °C. Additionally, the effects of some metal ions on the mannanase enzyme activity. Moreover, the clarifying efficiency of purified mannanase enzyme with some fruit juices such as orange, apricot, grape and apple was also investigated. Enzymatic treatment was carried out with 1 mL L(-1) of purified mannanase for 1 h at 60 °C. It was determined that the highest pure enzyme was efficient upon clarifying the apple juice at 154 % rate.

Algoriphagus trabzonensis sp. nov., isolated from freshwater, and emended description of Algoriphagus alkaliphilus

A Gram-staining-negative, non-motile, catalase- and oxidase-positive strain, designated MS7T, was isolated from freshwater of a river near Trabzon, Turkey. Its taxonomy was investigated using a polyphasic approach. The strain grew optimally at 28 °C and pH 7.5 and in the presence of 2.0 % NaCl. 16S rRNA gene sequence analysis revealed that the strain belonged to the genus Algoriphagus; strain MS7T showed highest sequence similarity to the type strains of Algoriphagus alkaliphilus (97.3 %), Algoriphagus terrigena (96.8 %), Algoriphagus jejuensis (96.2 %), Algoriphagus boritolerans (96.1 %) and Algoriphagus aquatilis (95.8 %). The major fatty acids of strain MS7T were iso-C15 : 0 (30.14 %) and summed future 9 (10-methyl C16 : 0 and/or iso-C17 : 1 ω9c 18.75 %). Polar lipid analysis revealed phosphatidylethanolamine, a variety of unidentified lipids, an unidentified aminophospholipid, an unidentified phospholipid and an unidentified aminolipid. The major isoprenoid quinone was MK-7.The DNA G+C content of MS7T was 41.6 mol%, a value consistent with that of members of the genus Algoriphagus. The level of DNA–DNA relatedness between strain MS7T and A. alkaliphilus LMG 22694T was 41 %, which is clearly below the 70 % threshold accepted for species delineation. Thus, our results support the placement of strain MS7T within a separate and previously unrecognized species. On the basis of these data, the strain is considered to represent a novel species of the genus Algoriphagus, for which the name Algoriphagus trabzonensis sp. nov. is proposed. The type strain is MS7T ( = NCCB 100372T = LMG 26290T). An emended description of A. alkaliphilus is also provided.

Molecular Phylogenetic Diversity and Spatial Distribution of Bacterial Communities in Cooling Stage during Swine Manure Composting

Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and subsequent sub-cloning and sequencing were used in this study to analyze the molecular phylogenetic diversity and spatial distribution of bacterial communities in different spatial locations during the cooling stage of composted swine manure. Total microbial DNA was extracted, and bacterial near full-length 16S rRNA genes were subsequently amplified, cloned, RFLP-screened, and sequenced. A total of 420 positive clones were classified by RFLP and near-full-length 16S rDNA sequences. Approximately 48 operational taxonomic units (OTUs) were found among 139 positive clones from the superstratum sample; 26 among 149 were from the middle-level sample and 35 among 132 were from the substrate sample. Thermobifida fusca was common in the superstratum layer of the pile. Some Bacillus spp. were remarkable in the middle-level layer, and Clostridium sp. was dominant in the substrate layer. Among 109 OTUs, 99 displayed homology with those in the GenBank database. Ten OTUs were not closely related to any known species. The superstratum sample had the highest microbial diversity, and different and distinct bacterial communities were detected in the three different layers. This study demonstrated the spatial characteristics of the microbial community distribution in the cooling stage of swine manure compost.

Thermotolerant Bacillus kokeshiiformis sp. nov. isolated from marine animal resources compost

A novel Gram-staining-positive, endospore-forming, rod-shaped, facultatively anaerobic, thermotolerant bacterium, designated strain MO-04T, was isolated from a marine animal resources (MAR) compost. The 16S rRNA gene sequence of strain MO-04T showed 99.4 % similarity with Bacillus thermolactis R-6488T, 94.1 % similarity with Bacillus thermoamylovorans CNCM I-1378T, 93.3 % similarity with Bacillus humi LMG 22167T, 93.2 % similarity with Bacillus niacini IFO 15566T and the similarities with other species were less than 93 %. DNA–DNA relatedness between strain MO-04T and B. thermolactis DSM 23332T was 45 %. The DNA G+C content of strain MO-04T was 33.4 mol%, comparatively lower than that of B. thermolactis R-6488T (35.0 mol%). Strain MO-04T grew at 35–61 °C (optimum 50 °C), pH 4.5–9.0 (optimum pH 7.2) and tolerated up to 8.0 % (w/v) NaCl (optimum 2 %). The MO-04T cell wall peptidoglycan type was meso-2,6-diaminopimelic acid, and the major fatty acids were C16 : 1, C14 : 1, C17 : 0 and C17 : 1. The major polar lipids were represented by diphosphatidylglycerol and phosphatidylglycerol and two unidentified phospholipids. The analysed polyphasic data presented here clearly indicate that the isolate MO-04T is considered to represent a novel species within the genus Bacillus for which the name Bacillus kokeshiiformis sp. nov. is proposed. The type strain of B. kokeshiiformis is MO-04T ( = JCM 19325T = KCTC 33163T).

Screening of bacterial biocontrols against sapstain fungus (Lasiodiplodia theobromae Pat.) of rubberwood (Hevea brasiliensis Muell.Arg.)

Diverse bacterial biocontrol agents from various sources of aerobic composts against the sapstain fungus Lasiodiplodia theobromae in rubberwood (Hevea brasiliensis) were isolated, screened and identified by various morphological, biochemical and molecular techniques. The inhibitory effect of seventeen bacterial isolates was examined and seven exhibited inhibition towards the sapstain fungus. Among the seven antagonists, six were conclusively identified as Bacillus subtilis and one as Paenibacillus polymyxa using 16S rRNA-encoding gene sequencing. This is the first report on the occurrence of P. polymyxa, a potent biofertilizer and antagonist in vermicompost. HiCrome Bacillus agar was identified as an effective medium for differentiation of B. subtilis from other Bacillus species. The present work demonstrates the efficacy of the antagonistic property of B. subtilis strains against rubberwood sapstain fungus. Culture-based antagonistic inhibition displayed by B. subtilis can be extended to cater to the biocontrol requirements of wood-based industries against the stain fungus. The study showed the utility of an integrated approach, employing morphological, biochemical and molecular tools for conclusive identification of several bacterial isolates present in aerobic composts from diverse sources.

Isolation and Characterization of Novel Denitrifying Bacterium Geobacillus sp. SG-01 Strain from Wood Chips Composted with Swine Manure

Nitrate contamination in ground and surface water is an increasingly serious environmental problem and only a few bacterial strains have been identified that have the ability to remove nitrogen pollutants from wastewater under thermophilic conditions. We therefore isolated thermophilic facultative bacterial strains from wood chips that had been composted with swine manure under aerated high temperature conditions so as to identify strains with denitrifying ability. Nine different colonies were screened and 3 long rod-shaped bacterial strains designated as SG-01, SG-02, and SG-03 were selected. The strain SG-01 could be differentiated from SG-02 and SG-03 on the basis of the method that it used for sugar utilization. The 16S rRNA genes of this strain also had high sequence similarity with Geobacillus thermodenitrificans 465^T (99.6%). The optimal growth temperatures (55°C), pH values (pH 7.0), and NaCl concentrations (1%) required for the growth of strain SG-01 were established. This strain reduced 1.18 mM nitrate and 1.45 mM nitrite in LB broth after 48 h of incubation. These results suggest that the G. thermodenitrificans SG-01 strain may be useful in the removal of nitrates and nitrites from wastewater generated as a result of livestock farming.

Compost: its role, mechanism and impact on reducing soil-borne plant diseases

Soil-borne plant pathogens are responsible for causing many crop plant diseases, resulting in significant economic losses. Compost application to agricultural fields is an excellent natural approach, which can be taken to fight against plant pathogens. The application of organic waste products is also an environmentally friendly alternative to chemical use, which unfortunately is the most common approach in agriculture today. This review analyses pioneering and recent compost research, and also the mechanisms and mode of action of compost microbial communities for reducing the activity of plant pathogens in agricultural crops. In addition, an approach for improving the quality of composts through the microbial communities already present in the compost is presented. Future agricultural practices will almost definitely require integrated research strategies to help combat plant diseases.

Structure of the homodimeric glycine decarboxylase P-protein from Synechocystis sp. PCC 6803 suggests a mechanism for redox regulation

Glycine decarboxylase, or P-protein, is a pyridoxal 5'-phosphate (PLP)-dependent enzyme in one-carbon metabolism of all organisms, in the glycine and serine catabolism of vertebrates, and in the photorespiratory pathway of oxygenic phototrophs. P-protein from the cyanobacterium Synechocystis sp. PCC 6803 is an α2 homodimer with high homology to eukaryotic P-proteins. The crystal structure of the apoenzyme shows the C terminus locked in a closed conformation by a disulfide bond between Cys(972) in the C terminus and Cys(353) located in the active site. The presence of the disulfide bridge isolates the active site from solvent and hinders the binding of PLP and glycine in the active site. Variants produced by substitution of Cys(972) and Cys(353) by Ser using site-directed mutagenesis have distinctly lower specific activities, supporting the crucial role of these highly conserved redox-sensitive amino acid residues for P-protein activity. Reduction of the 353-972 disulfide releases the C terminus and allows access to the active site. PLP and the substrate glycine bind in the active site of this reduced enzyme and appear to cause further conformational changes involving a flexible surface loop. The observation of the disulfide bond that acts to stabilize the closed form suggests a molecular mechanism for the redox-dependent activation of glycine decarboxylase observed earlier.

Sequence-based analysis of the bacterial and fungal compositions of multiple kombucha (tea fungus) samples

Kombucha is a sweetened tea beverage that, as a consequence of fermentation, contains ethanol, carbon dioxide, a high concentration of acid (gluconic, acetic and lactic) as well as a number of other metabolites and is thought to contain a number of health-promoting components. The sucrose-tea solution is fermented by a symbiosis of bacteria and yeast embedded within a cellulosic pellicle, which forms a floating mat in the tea, and generates a new layer with each successful fermentation. The specific identity of the microbial populations present has been the focus of attention but, to date, the majority of studies have relied on culture-based analyses. To gain a more comprehensive insight into the kombucha microbiota we have carried out the first culture-independent, high-throughput sequencing analysis of the bacterial and fungal populations of 5 distinct pellicles as well as the resultant fermented kombucha at two time points. Following the analysis it was established that the major bacterial genus present was Gluconacetobacter, present at >85% in most samples, with only trace populations of Acetobacter detected (<2%). A prominent Lactobacillus population was also identified (up to 30%), with a number of sub-dominant genera, not previously associated with kombucha, also being revealed. The yeast populations were found to be dominated by Zygosaccharomyces at >95% in the fermented beverage, with a greater fungal diversity present in the cellulosic pellicle, including numerous species not identified in kombucha previously. Ultimately, this study represents the most accurate description of the microbiology of kombucha to date.

Diversity of bacterial isolates during full scale rotary drum composting

Bacterial diversity of full scale rotary drum composter from biodegradable organic waste samples were analyzed through two different approaches, i.e., Culture dependent and independent techniques. Culture-dependent enumerations for indigenous population of bacterial isolates mainly total heterotrophic bacteria (Bacillus species, Pseudomonas species and Enterobacter species), Fecal Coliforms, Fecal Streptococci, Escherichia coli, Salmonella species and Shigella species showed reduction during the composting period. On the other hand, Culture-independent method using PCR amplification of specific 16S rRNA sequences identified the presence of Acinetobacter species, Actinobacteria species, Bacillus species, Clostridium species, Hydrogenophaga species, Butyrivibrio species, Pedobacter species, Empedobactor species and Flavobacterium species by sequences clustering in the phylogenetic tree. Furthermore, correlating physico-chemical analysis of samples with bacterial diversity revealed the bacterial communities have undergone changes, possibly linked to the variations in temperature and availability of new metabolic substrates while decomposing organics at different stages of composting.

Bacteriophage P23-77 capsid protein structures reveal the archetype of an ancient branch from a major virus lineage

It has proved difficult to classify viruses unless they are closely related since their rapid evolution hinders detection of remote evolutionary relationships in their genetic sequences. However, structure varies more slowly than sequence, allowing deeper evolutionary relationships to be detected. Bacteriophage P23-77 is an example of a newly identified viral lineage, with members inhabiting extreme environments. We have solved multiple crystal structures of the major capsid proteins VP16 and VP17 of bacteriophage P23-77. They fit the 14 Å resolution cryo-electron microscopy reconstruction of the entire virus exquisitely well, allowing us to propose a model for both the capsid architecture and viral assembly, quite different from previously published models. The structures of the capsid proteins and their mode of association to form the viral capsid suggest that the P23-77-like and adeno-PRD1 lineages of viruses share an extremely ancient common ancestor.

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High-resolution structures of the two major capsid proteins of bacteriophage P23-77

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P23-77 capsid proteins exhibit a conserved single β-barrel core fold

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P23-77 is an ancient relative of the double β-barrel lineage of viruses

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Capsid model illustrates that P23-77 uses a novel method of organization

Effect of initial moisture content on the in-vessel composting under air pressure of organic fraction of municipal solid waste in Morocco

This study aimed to evaluate the effect of initial moisture content on the in-vessel composting under air pressure of organic fraction of municipal solid waste in Morocco in terms of internal temperature, produced gases quantity, organic matter conversion rate, and the quality of the final composts.

For this purpose, in-vessel bioreactor was designed and used to evaluate both appropriate initial air pressure and appropriate initial moisture content for the composting process. Moreover, 5 experiments were carried out within initial moisture content of 55%, 65%, 70%, 75% and 85%. The initial air pressure and the initial moisture content of the mixture showed a significant effect on the aerobic composting. The experimental results demonstrated that for composting organic waste, relatively high moisture contents are better at achieving higher temperatures and retaining them for longer times.

This study suggested that an initial moisture content of around 75%, under 0.6 bar, can be considered as being suitable for efficient composting of organic fraction of municipal solid waste. These last conditions, allowed maximum value of temperature and final composting product with good physicochemical properties as well as higher organic matter degradation and higher gas production. Moreover, final compost obtained showed good maturity levels and can be used for agricultural applications.

An optimized DNA extraction and purification method from dairy manure compost for genetic diversity analysis

An unbiased DNA extraction protocol is necessary for analysis of genetic diversity, particularly, of genes in complex environmental samples by nucleic acid techniques. In the present study, three manual extraction methods and two commonly used commercial kits, which were accompanied by two DNA purification strategies, were compared based on cell lysis efficiency, DNA and humic acid yields, PCR amplification and denaturing gradient gel electrophoresis (DGGE) analysis. The results show that in spite of higher cell lysis efficiencies of the two commercial kits, the purified DNA yields were only one-third of that obtained by the two manual methods of FTSP (Freeze-thaw-SDS-Protein K) and FTSPP (Freeze-thaw-SDS-Protein K-Polyvinylpolypyrrolidone). The purified DNA from all five methods was pure enough for successful PCR and real-time PCR amplifications in the presence of 1 μg μL(-1) BSA. However, the FTSPP extraction method with DNA purification by a Wizard(®) kit yielded the largest number of 16S rRNA gene copies and ribotypes or bands in DGGE profiles, which indicated a superiority over the other four methods. The development of this optimized DNA extraction and purification method may provide a valuable tool for further molecular analysis of compost.

An improved sequence-aided T-RFLP analysis of bacterial succession during oyster mushroom substrate preparation

While oyster mushroom (Pleurotus spp.) is one of the most popular cultivated edible mushrooms, there is scanty information about the microbial community taking part in mushroom substrate production. In this study, an improved sequence-aided terminal restriction fragment length polymorphism (T-RFLP) was used to identify and (semi-)quantify the dominant bacteria of oyster mushroom substrate preparation. The main features of the improved T-RFLP data analysis were the alignment of chromatograms with variable clustering thresholds, the visualization of data matrix with principal component analysis ordination superimposed with cluster analysis, and the search for stage-specific peaks (bacterial taxa) with similarity percentage (analysis of similarity) analysis, followed by identification with clone libraries. By applying this method, the dominance of the following bacterial genera was revealed during oyster mushroom substrate preparation: Pseudomonas and Sphingomonas at startup, Bacillus, Geobacillus, Ureibacillus, Pseudoxanthomonas, and Thermobispora at the end of partial composting, and finally several genera of Actinobacteria, Thermus, Bacillus, Geobacillus, Thermobacillus, and Ureibacillus in the mature substrate. As the proportion of uncultured bacteria increased during the process, it is worth establishing strain collections from partial composting and from mature substrate for searching new species.