Thermophilic and alkaliphilic Actinobacteria: biology and potential applications

Sediment microbial diversity, functional potentials, and antibiotic resistance pattern: a case study of Cochin Estuary core sediment

Marine sediments are an important part of the marine environment and the world's greatest organic carbon source. Sediment microorganisms are important regulators of major geochemical and eco-environmental processes in marine environments, especially nutrient dynamics and biogeochemical cycles. Despite their importance, core marine microorganisms are virtually unknown due to a lack of consensus on how to identify them. Most core microbiotas have been characterized thus far based on species abundance and occurrence. The combined effects of habitat and depth on benthic bacterial communities and ecological functions were studied using "Next-Generation sequencing (NGS) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) predictive functional profiling" at the surface (0.2 cm) and bottom depth (250 cm) in a sediment core sample from Cochin Estuary, Kerala, India. The results showed that bacterial diversity and richness were significantly higher in the surface sediment sample with the most abundant phyla being Proteobacteria, Acidobacteria, Chloroflexi, and Bacteroidetes. The major metabolic functions were metabolism, followed by environmental information processing and genetic information processing. Antibiotic resistance genes between the surface and bottom samples help to understand the resistance pattern among multidrug resistance is the most prominent one. Among viruses, Siphoviridae is the dominant family, followed by Myoviridae. In the case of Archea, Crenarchaeota is dominant, whereas among eukaryotes phyla Streptophyta and Chordata were dominant in the surface and the bottom samples respectively.

Harnessing bacterial endophytes for environmental resilience and agricultural sustainability

In the current era of environmental disasters and the necessity of sustainable development, bacterial endophytes have gotten attention for their role in improving agricultural productivity and ecological sustainability. This review explores the multifaceted contributions of bacterial endophytes to plant health and ecosystem sustainability. Bacterial endophytes are invaluable sources of bioactive compounds, promising breakthroughs in medicine and biotechnology. They also serve as natural biocontrol agents, reducing the need for synthetic fertilizers and fostering environmentally friendly agricultural practices. It provides eco-friendly solutions that align with the necessity of sustainability since they can improve pest management, increase crop resilience, and facilitate agricultural production. This review also underscores bacterial endophytes' contribution to promoting sustainable and green industrial productions. It also presented how incorporating these microorganisms into diverse industrial sectors can harmonize humankind with ecological stability. The potential of bacterial endophytes has been largely untapped, presenting an opportunity for pioneering advancements in sustainable industrial applications. Their importance caught attention as they provided innovative solutions to the challenging problems of the new era. This review sheds light on the remarkable potential of bacterial endophytes in various industrial sectors. Further research is imperative to discover their multifaceted potential. It will be essential to delve deeper into their mechanisms, broaden their uses, and examine their long-term impacts.

Differences in the constituents of bacterial microbiota of soils collected from two fields of diverse potato blackleg and soft rot diseases incidences, a case study

The presence of bacteria from the Dickeya spp. and Pectobacterium spp. in farmlands leads to global crop losses of over $420 million annually. Since 1982, the scientists have started to suspect that the development of disease symptoms in crops might be inhibited by bacteria present in the soil. Here, we characterized in terms of physicochemical properties and the composition of bacterial soil microbiota two fields differing, on the basis of long-term studies, in the occurrence of Dickeya spp.- and Pectobacterium spp.-triggered infections. Majority, i.e. 17 of the investigated physicochemical features of the soils collected from two fields of either low or high potato blackleg and soft rot diseases incidences turned out to be similar, in contrast to the observed 4 deviations in relation to Mg, Mn, organic C and organic substance contents. By performing microbial cultures and molecular diagnostics-based identification, 20 Pectobacterium spp. strains were acquired from the field showing high blackleg and soft rot incidences. In addition, 16S rRNA gene amplicon sequencing followed by bioinformatic analysis revealed differences at various taxonomic levels in the soil bacterial microbiota of the studied fields. We observed that bacteria from the genera Bacillus, Rumeliibacillus, Acidobacterium and Gaiella turned out to be more abundant in the soil samples originating from the field of low comparing to high frequency of pectinolytic bacterial infections. In the herein presented case study, it is shown for the first time that the composition of bacterial soil microbiota varies between two fields differing in the incidences of soft rot and blackleg infections.

Compost-diatomite-based phytostabilization course under extreme environmental conditions in terms of high pollutant contents and low temperatures

The effects of changes in environmental temperatures on the immobilization or removal of cationic potentially toxic elements (PTE) in heavily polluted soils are often poorly understood, although both are widely studied in the context of phytostabilization. To address this issue, a novel compost-diatomite hybrid (CDH) amendment was developed and applied for assisted phytostabilization at two external temperature regimes. (Cd/Ni/Cu/Zn)-extremely polluted soils (unenriched and CDH-enriched) were cultivated with perennial ryegrass and native soil microbiome under greenhouse conditions and then transferred to freeze-thaw conditions (FTC). The decrease in metal potential toxicity in soils subjected to phytostabilization following both temperature treatments was characterized by a combination of sequential extraction and atomic absorption measurements. The soil microbiome was characterized by high-throughput sequencing. In a relative comparison, the greatest decrease in the content of all PTEs in CDH-enriched soil (compared to unenriched soil) appeared in FTC. Furthermore, under the influence of FTC, in the relative comparison between two CDH-enriched soils (exposed-, and not-exposed- to FTC) and two unenriched soils (exposed-, and not-exposed- to FTC), the content of all PTEs decreased more sharply in the CDH-enriched series than in the unenriched series. The largest redistribution into four sequentially extracted fractions in CDH-enriched soil was found for Zn. Based on the distribution pattern, Zn immobilization was greater in CDH-enriched soil in FTC. CDH increased species richness in the soil, while FTC stimulated the growth of Bacteroidia, Alphaproteobacteria, Theromomicrobia, and Gammaproteobacteria. The analysis of the functionalities of the microbiome indicated enhanced metal transportation and defense systems in samples exposed to FTC. The current research is crucial for understanding how extreme environmental conditions in both cases high pollutant levels and low temperatures affect the movement and transformation of PTEs in polluted soils during phytostabilization.

Laboratory investigation and core flood demonstration of enhanced biogenic methane generation from lignite

Over the last several decades, coalbed methane (CBM) has emerged as an important energy source in developing nations like India as well as worldwide and is expected to play a significant role in the energy portfolio of the future. The current scenario of rapid exhaustion of fossil fuels is leading to the need to explore alternative and efficient fuel resources. The present study demonstrates enhanced methane production per gram of lignite (lowest-rank coal). Optimization of the bioconversion of lignite to methane revealed 55°C temperature and 1.5 g/L NaCl concentration as ambient conditions for the process. A scale-up study in the optimized condition showed 2,800 mM methane production per 25 g of lignite in anaerobic conditions. Further, Fourier transform Infrared (FTIR) and Gas Chromatography Mass Spectrometry (GCMS) analysis showed bioconversion of lignite into simpler intermediate substrates required for methane production. The results highlighted that the bacterial action first converts lignite into volatile fatty acids, which subsequently get converted into methane. Further, the exploration of indigenous microbial consortia in Tharad well (THAA) mainly comprises the order Methanosarcinales and Methanomicrobiales. The pathogenicity of the microbial consortium THAA was declared safe for use in mice via the oral route by The Energy and Resources Institute (TERI), India. The study demonstrated the development of indigenous consortia (TERI THAA), which can potentially enhance methane production from the lowest coal grade under extreme conditions in Indian coal beds.

Impact of artisanal refining activities on bacterial diversity in a Niger Delta fallow land

Hydrocarbon pollution is a major ecological problem facing oil-producing countries, especially in the Niger Delta region of Nigeria. In this study, a site that had been previously polluted by artisanal refining activity was investigated using 16S rRNA Illumina high-throughput sequencing technology and bioinformatics tools. These were used to investigate the bacterial diversity in soil with varying degrees of contamination, determined with a gas chromatography-flame ionization detector (GC-FID). Soil samples were collected from a heavily polluted (HP), mildly polluted (MP), and unpolluted (control sample, CS) portion of the study site. DNA was extracted using the Zymo Research (ZR) Fungi/Bacteria DNA MiniPrep kit, followed by PCR amplification and agarose gel electrophoresis. The microbiome was characterized based on the V3 and V4 hypervariable regions of the 16S rRNA gene. QIIME (Quantitative Insights Into Microbial Ecology) 2 software was used to analyse the sequence data. The final data set covered 20,640 demultiplexed high-quality reads and a total of 160 filtered bacterial OTUs. Proteobacteria dominated samples HP and CS, while Actinobacteria dominated sample MP. Denitratisoma, Pseudorhodoplanes, and Spirilospora were the leading genera in samples HP, CS, and MP respectively. Diversity analysis indicated that CS [with 25.98 ppm of total petroleum hydrocarbon (TPH)] is more diverse than HP (with 490,630 ppm of TPH) and MP (with 5398 ppm of TPH). A functional prediction study revealed that six functional modules dominated the dataset, with metabolism covering up to 70%, and 11 metabolic pathways. This study demonstrates that a higher hydrocarbon concentration in soil adversely impacts microbial diversity, creating a narrow bacterial diversity dominated by hydrocarbon-degrading species, in addition to the obvious land and ecosystem degradation caused by artisanal refining activities. Overall, the artisanal refining business is significantly driving ecosystem services losses in the Niger Delta, which calls for urgent intervention, with focus on bioremediation.

Industrial and Pharmaceutical Applications of Microbial Diversity of Hypersaline Ecology from Lonar Soda Crater

The unidentified geochemical and physiochemical characteristics of Soda Lakes across the globe make it a novel reservoir and bring attention to scientific civic for its conceivable industrial and pharmaceutical applications. In India, in the Maharashtra state, Lonar Lake is a naturally created Soda Lake by a meteorite impact. Phylogenetic data from this lake explored a diverse array of microorganisms like haloalkaliphilic bacteria and Archaea. Previously reported studies postulated the major microbial communities present in this lake ecosystem are Proteobacteria, Actinobacteria, Firmicutes, and Cyanobacteria. Furthermore, it also contains Bacteroidetes, Nitrospirae, and Verrucomicrobia. This lake is also rich in phytoplankton, with the predominant presence of the Spirulina plantensis. Unique microbial strains from Lonar Lake ecosystems have fascinated consideration as a source of biological molecules with medicinal, industrial, and biotechnological potential. Recent literature revealed the isolation of antibioticproducing bacteria and alkaline proteases-producing alkaliphilic bacterium, as well as novel species of rare methylotrophs, other bacterial strains involved in producing vital enzymes, and unique actinomycetes are also reported. It indicates that the novel bacterial assemblage not reached hitherto may exist in this modified and unique ecology. This comprehensive review provides information about microbial diversity and its industrial and pharmaceutical interests that exist in Lonar Lake, which could be the future source of bioactive enzymes, biosurfactants, and biofuel and also useful in bioremediation. Furthermore, the novel species of microorganisms isolated from Lonar Lake have applications in the biosynthesis of medicines like antibiotics, antivirals, antifungals, anti-inflammatory agents, and precursors for synthesising valuable products. Data consolidated in the present review will cater to the needs of emerging industrial sectors for their commercial and therapeutic applications.

Effect of freeze-thaw manipulation on phytostabilization of industrially contaminated soil with halloysite nanotubes

The latest trends in improving the performance properties of soils contaminated with potentially toxic elements (PTEs) relate to the possibility of using raw additives, including halloysite nanotubes (HNTs) due to eco-friendliness, and inexpensiveness. Lolium perenne L. was cultivated for 52 days in a greenhouse and then moved to a freezing-thawing chamber for 64 days. HNT addition into PTE-contaminated soil cultivated with grass under freezing-thawing conditions (FTC) was tested to demonstrate PTE immobilization during phytostabilization. The relative yields increased by 47% in HNT-enriched soil in a greenhouse, while under FTC decreased by 17% compared to the adequate greenhouse series. The higher PTE accumulation in roots in HNT presence was evident both in greenhouse and chamber conditions. (Cr/Cd and Cu)-relative contents were reduced in soil HNT-enriched-not-FTC-exposed, while (Cr and Cu) in HNT-enriched-FTC-exposed. PTE-immobilization was discernible by (Cd/Cr/Pb and Zn)-redistribution into the reducible fraction and (Cu/Ni and Zn) into the residual fraction in soil HNT-enriched-not-FTC-exposed. FTC and HNT facilitated transformation to the residual fraction mainly for Pb. Based on PTE-distribution patterns and redistribution indexes, HNT's role in increasing PTE stability in soils not-FTC-exposed is more pronounced than in FTC-exposed compared to the adequate series. Sphingomonas, Acidobacterium, and Mycobacterium appeared in all soils. HNTs mitigated FTC's negative effect on microbial diversity and increased Planctomycetia abundance.

Shotgun Metagenomics Reveals Impacts of Copper and Water Heater Anodes on Pathogens and Microbiomes in Hot Water Plumbing Systems

Hot water building plumbing systems are vulnerable to the proliferation of opportunistic pathogens (OPs), including Legionella pneumophila and Mycobacterium avium. Implementation of copper as a disinfectant could help reduce OPs, but a mechanistic understanding of the effects on the microbial community under real-world plumbing conditions is lacking. Here, we carried out a controlled pilot-scale study of hot water systems and applied shotgun metagenomic sequencing to examine the effects of copper dose (0-2 mg/L), orthophosphate corrosion control agent, and water heater anode materials (aluminum vs magnesium vs powered anode) on the bulk water and biofilm microbiome composition. Metagenomic analysis revealed that, even though a copper dose of 1.2 mg/L was required to reduce Legionella and Mycobacterium numbers, lower doses (e.g., ≤0.6 mg/L) measurably impacted the broader microbial community, indicating that the OP strains colonizing these systems were highly copper tolerant. Orthophosphate addition reduced bioavailability of copper, both to OPs and to the broader microbiome. Functional gene analysis indicated that both membrane damage and interruption of nucleic acid replication are likely at play in copper inactivation mechanisms. This study identifies key factors (e.g., orthophosphate, copper resistance, and anode materials) that can confound the efficacy of copper for controlling OPs in hot water plumbing.

Comparison of bacterial and fungal communities structure and dynamics during chicken manure and pig manure composting

Composting is a sustainable and eco-friendly technology that turns animal waste into organic fertilizers. It remains unclear whether differences exist in the structure of microbial communities during different livestock manure composting. This study analyzed the dynamic change of bacterial and fungal communities, metabolic function, and trophic mode during chicken manure (CM) and pig manure (PM) composting based on 16S rRNA and ITS sequencing. Environmental factors were investigated for their impact on microbial communities. During composting, bacterial diversity decreased and then increased, while fungal diversity slightly increased and then decreased. Saccharomonospora and Aspergillus were the dominant genera and key microorganisms in CM and PM, respectively, which played crucial roles in sustaining the stability of the ecological network structure in the microbial ecology and participating in metabolism. Saccharomonospora gradually increased, while Aspergillus increased at first and then decreased. PM had better microbial community stability and more keystone taxa than CM. In CM and PM, the primary function of bacterial communities was metabolism, while saprotroph was the primary trophic mode of fungal communities. Dissolved organic carbon (DOC) was the primary factor influencing the structure and function of microbial communities in CM and PM. In addition to DOC, pH and moisture were important factors affecting the fungal communities in CM and PM, respectively. These results show that the succession of bacteria and fungi in CM and PM proceeded in a similar pattern, but there are still some differences in the dominant genus and their responses to environmental factors.

Potentiality of Actinomycetia Prevalent in Selected Forest Ecosystems in Assam, India to Combat Multi-Drug-Resistant Microbial Pathogens

Actinomycetia are known for their ability to produce a wide range of bioactive secondary metabolites having significant therapeutic importance. This study aimed to explore the potential of actinomycetia as a source of bioactive compounds with antimicrobial properties against multi-drug-resistant (MDR) clinical pathogens. A total of 65 actinomycetia were isolated from two unexplored forest ecosystems, namely the Pobitora Wildlife Sanctuary (PWS) and the Deepor Beel Wildlife Sanctuary (DBWS), located in the Indo-Burma mega-biodiversity hotspots of northeast India, out of which 19 isolates exhibited significant antimicrobial activity. 16S rRNA gene sequencing was used for the identification and phylogenetic analysis of the 19 potent actinomycetia isolates. The results reveal that the most dominant genus among the isolates was Streptomyces (84.21%), followed by rare actinomycetia genera such as Nocardia, Actinomadura, and Nonomuraea. Furthermore, seventeen of the isolates tested positive for at least one antibiotic biosynthetic gene, specifically type II polyketide synthase (PKS-II) and nonribosomal peptide synthetases (NRPSs). These genes are associated with the production of bioactive compounds with antimicrobial properties. Among the isolated strains, three actinomycetia strains, namely Streptomyces sp. PBR1, Streptomyces sp. PBR36, and Streptomyces sp. DBR11, demonstrated the most potent antimicrobial activity against seven test pathogens. This was determined through in vitro antimicrobial bioassays and the minimum inhibitory concentration (MIC) values of ethyl acetate extracts. Gas chromatography-mass spectrometry (GS-MS) and whole-genome sequencing (WGS) of the three strains revealed a diverse group of bioactive compounds and secondary metabolite biosynthetic gene clusters (smBGCs), respectively, indicating their high therapeutic potential. These findings highlight the potential of these microorganisms to serve as a valuable resource for the discovery and development of novel antibiotics and other therapeutics with high therapeutic potential.

l-Asparaginase producing novel Streptomyces sp. HB2AG: optimization of process parameters and whole genome sequence analysis

l-asparaginase (ASNase) is a key enzyme widely used as an anti-cancer drug and is also used in the pharmaceutical and food processing industries. This enzyme's applications are determined by its source and nature. The production of the enzyme through the fermentation process is also crucial for economic feasibility. Searching for a new potent microbial strain is necessary for increased ASNase synthesis. In this work, a potent strain was isolated from the sediment of Chilika Lake and selected for its high ASNase production potential. It was recognized following Bergey's manual of determinative and phylogenetic analysis was carried out by 16S rDNA sequencing. The isolated organism was Streptomyces sp. HB2AG. Additionally, a genome-wide analysis of HB2AG was performed. The result showed that the HB2AG genome possesses a chromosome with 6,099,956 bp and GC content of 74.0%. The whole genome analysis of the strain HB2AG revealed the presence of ASNase (ansA, ansB) and Asparagine synthase (asnB) in the HB2AG genome. Optimization of media composition is crucial for microbial growth and obtaining the desired end product. The current effort focuses on the Taguchi orthogonal design to determine optimum factor combinations that would allow the strain to produce maximum ASNase enzyme. Results showed that compared to unoptimized media, approximately 1.76-fold higher ASNase production was observed in Sea Water Luria Bertani (SWLB) media, pH-5, 0.5% (w/v) of lactose, 0.5% (w/v) of casein, 2.5% (w/v) NaCl, 1 mM Ca2+ and 0.1% Tween 80.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03620-0.

Effects of cornstalk and sawdust coverings on greenhouse gas emissions during sheep manure storage

Manure covered by organic materials during the storage has shown that it can effectively reduce emissions of greenhouse gases, but few studies have focused on the bacterial communities in manure or the coverage and mechanism responsible for reducing gas emissions. Therefore, this study investigated the impacts and mechanisms of cornstalk and sawdust coverings on greenhouse gas emissions during sheep manure storage. Sheep manure covered by organic material reduced nitrous oxide (N₂O) emissions (42.27%-42.55%) relative to uncovered control through physical adsorption and biological transformation of Acinetobacter, Corynebacterium, Brachybacterium, Dietzia and Brevibacterium. Sheep manure covered by organic materials also increased methane (CH₄) emissions (16.31%-43.07%) by increasing anaerobic zones of coverage. Overall, coverings reduced carbon dioxide equivalent (CO₂eq) by 29.87%-33.60%. Coverings had less effect on the bacterial diversity and community of sheep manure, and the number of bacteria shared by sheep manure and the covering material increased with storage progress, indicating that these bacteria were transferred to the covering materials with gas emissions and moisture volatilization. Fourier-transform infrared spectroscopy (FTIR) and scanning electron microscopy (SEM) images showed that functional group intensities of the covering materials increased and the fibrous structures became more disordered during the storage period. In general, it was safe to use organic materials as coverages during sheep manure storage, which was conducive to reducing greenhouse gas emissions.

Antarctic Ardley Island terrace - An ideal place to study the marine to terrestrial succession of microbial communities

The study of chronosequences is an effective tool to study the effects of environmental changes or disturbances on microbial community structures, diversity, and the functional properties of ecosystems. Here, we conduct a chronosequence study on the Ardley Island coastal terrace of the Fildes Peninsula, Maritime Antarctica. The results revealed that prokaryotic microorganism communities changed orderly among the six successional stages. Some marine microbial groups could still be found in near-coastal soils of the late stage (lowest stratum). Animal pathogenic bacteria and stress-resistant microorganisms occurred at the greatest level with the longest succession period. The main driving factors for the succession of bacteria, archaea, and fungi along Ardley Island terrace were found through Adonis analysis (PERMANOVA). During analysis, soil elements Mg, Si, and Na were related to the bacterial and archaeal community structure discrepancies, while Al, Ti, K, and Cl were related to the fungal community structure discrepancies. On the other hand, other environmental factors also play an important role in the succession of microbial communities, which could be different among each microorganism. The succession of bacterial communities is greatly affected by pH and water content; archaeal communities are greatly affected by N H 4 + ; fungal communities are affected by nutrients such as N O 3 - . In the analysis of the characteristic microorganisms along terrace, the succession of microorganisms was found to be influenced by complex and comprehensive factors. For instance, environmental instability, relationship with plants and ecological niches, and environmental tolerance. The results found that budding reproduction and/or with filamentous appendages bacteria were enriched in the late stage, which might be connected to its tolerance to rapid changes and barren environments. In addition, the decline in ammonia oxidation capacity of Thaumarchaeota archaeade with succession and the evolution of the fungi-plant relationship throughout classes were revealed. Overall, this research improves the understanding of the effect of the marine-to-terrestrial transition of the Ardley Island terrace on microbial communities. These findings will lay the foundation for more in-depth research regarding microbial adaptations and evolutionary mechanisms throughout the marine-terrestrial transition in the future.

Interplay of Gut Microbiota in Polycystic Ovarian Syndrome: Role of Gut Microbiota, Mechanistic Pathways and Potential Treatment Strategies

Polycystic Ovarian Syndrome (PCOS) comprises a set of symptoms that pose significant risk factors for various diseases, including type 2 diabetes, cardiovascular disease, and cancer. Effective and safe methods to treat all the pathological symptoms of PCOS are not available. The gut microbiota has been shown to play an essential role in PCOS incidence and progression. Many dietary plants, prebiotics, and probiotics have been reported to ameliorate PCOS. Gut microbiota shows its effects in PCOS via a number of mechanistic pathways including maintenance of homeostasis, regulation of lipid and blood glucose levels. The effect of gut microbiota on PCOS has been widely reported in animal models but there are only a few reports of human studies. Increasing the diversity of gut microbiota, and up-regulating PCOS ameliorating gut microbiota are some of the ways through which prebiotics, probiotics, and polyphenols work. We present a comprehensive review on polyphenols from natural origin, probiotics, and fecal microbiota therapy that may be used to treat PCOS by modifying the gut microbiota.

Metabolomic profiles of the liquid state fermentation in co-culture of Eurotium amstelodami and Bacillus licheniformis

As an important source of new drug molecules, secondary metabolites (SMs) produced by microorganisms possess important biological activities, such as antibacterial, anti-inflammatory, and hypoglycemic effects. However, the true potential of microbial synthesis of SMs has not been fully elucidated as the SM gene clusters remain silent under laboratory culture conditions. Herein, we evaluated the inhibitory effect of Staphylococcus aureus by co-culture of Eurotium amstelodami and three Bacillus species, including Bacillus licheniformis, Bacillus subtilis, and Bacillus amyloliquefaciens. In addition, a non-target approach based on ultra-performance liquid chromatography time-of-flight mass spectrometry (UPLC-TOF-MS) was used to detect differences in extracellular and intracellular metabolites. Notably, the co-culture of E. amstelodami and Bacillus spices significantly improved the inhibitory effect against S. aureus, with the combination of E. amstelodami and B. licheniformis showing best performance. Metabolomics data further revealed that the abundant SMs, such as Nummularine B, Lucidenic acid E2, Elatoside G, Aspergillic acid, 4-Hydroxycyclohexylcarboxylic acid, Copaene, and Pipecolic acid were significantly enhanced in co-culture. Intracellularly, the differential metabolites were involved in the metabolism of amino acids, nucleic acids, and glycerophospholipid. Overall, this work demonstrates that the co-culture strategy is beneficial for inducing biosynthesis of active metabolites in E. amstelodami and B. licheniformis.

Microbial community and predictive functionalities associated with the marine sediment of Coastal Gujarat

Marine sediments are complex ecosystems where structures and functions constantly change due to natural and anthropogenic influences. In this investigation, a comprehensive and comparative analysis of the bacterial communities and their functional potential of the pristine and polluted marine sediments were carried out using MiSeq. The phylum Proteobacteria was dominant in all study sites. Other phyla were Actinobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, Chloroflexi, Nitrospirae, Cyanobacteria, Verrucomicrobia, Tenericutes, and Chlorobi. Interestingly, about 50% of genera belong to the unclassified categories. The key genera were identified as Acinetobacter, Bacillus, Pseudomona, Idiomarina, Thalassospira, and Marinobacter, Halomonas, Planctomyces, Psychrobacter, and Vogesella. PICRUSt analysis revealed that major functions are associated with the metabolism category. Additionally, metabolism related to amino acids, carbohydrates, energy generation, xenobiotics degradation, nitrogen, sulfate, and methane were prominent. Similarly, the predicted metabolisms by COG and KEGG were observed in the microbial communities of the marine sediments. To date, a comprehensive description of the microbial life with metabolic potential in these study sites has not been investigated. This study therefore significantly adds to our understanding of the microbiome and its functional attributes of marine sediments.

Quinone redox cycling drives lignocellulose depolymerization and degradation in composting environments based on metagenomics analysis

In this study, the effect of Fe³⁺ on the quinone redox cycling driving lignocellulosic degradation in composting systems was investigated. The results showed that the degradation rates of cellulose, hemicellulose, and lignin were higher in the experimental group (CT) with Fe₂(SO₄)₃ addition than in the blank group (CK) (CT, 52.55 %, 45.14 %, 56.98 %; CK, 49.63 %, 37.34 %, 52.3 %). Changes in the abundance of key enzymes for quinone reduction (AA3_1, AA3_2, AA6) and the structural succession of microbial communities were analyzed by metagenomic analysis. Among them, Fe₂(SO₄)₃ had the most significant effect on AA3_2, with an approximately 8-fold increase in abundance compared to the beginning of composting. The dominant phylum in the composting process was Actinobacteria. In conclusion, the addition of Fe₂(SO₄)₃ contributed to the quinone redox cycling and effectively improved the degradation rate of lignocellulose in composting.

Quantitative metaproteomics reveals composition and metabolism characteristics of microbial communities in Chinese liquor fermentation starters

Introduction

Daqu, the Chinese liquor fermentation starter, contains complex microbial communities that are important for the yield, quality, and unique flavor of produced liquor. However, the composition and metabolism of microbial communities in the different types of high-temperature Daqu (i.e., white, yellow, and black Daqu) have not been well understood.

Methods

Herein, we used quantitative metaproteomics based on data-independent acquisition (DIA) mass spectrometry to analyze a total of 90 samples of white, yellow, and black Daqu collected in spring, summer, and autumn, revealing the taxonomic and metabolic profiles of different types of Daqu across seasons.

Results

Taxonomic composition differences were explored across types of Daqu and seasons, where the under-fermented white Daqu showed the higher microbial diversity and seasonal stability. It was demonstrated that yellow Daqu had higher abundance of saccharifying enzymes for raw material degradation. In addition, considerable seasonal variation of microbial protein abundance was discovered in the over-fermented black Daqu, suggesting elevated carbohydrate and amino acid metabolism in autumn black Daqu.

Discussion

We expect that this study will facilitate the understanding of the key microbes and their metabolism in the traditional fermentation process of Chinese liquor production.

Microbiological analysis, antimicrobial activity, heavy-metals content and physico-chemical properties of Fijian mud pool samples

The hot springs are home to a rich bacterial diversity which could be the source of enzymes, antibiotics and many other commercially important products. Most of the hot springs present in Fiji are unexplored and their analysis of microbial diversity could be of great interest in facilitating various industrial, agricultural and medicinal applications. This study is an attempt to evaluate the heavy metal concentration and to analyze the comprehensive bacterial diversity of two Fijian thermal mud pools, namely Sabeto and Tifajek. The two hot springs have a pH of 7.28 to 7.19 and a temperature of 32.2 to 38.8 °C, respectively. Mean metal concentrations of the studied mud samples ranged from 4.758 to 6.870 mg/kg and followed a decreasing sequence as Fe > Mn > Zn > Na > Ni > Cd > Ca > Cr > Cu. Levels of Fe, Na, Mn, Zn, Ni, Cd, Ca, Cr, Cu in the mud pool samples were within World Health Organisation (WHO) limits, while Cd was above regulatory limits. The heavy metals analysis results showed that both mud pools had high values for Cd, above the WHO limit of 3 mg/kg. In addition, 8 strains of actinomycetes were successfully identified for the first time in the Sabeto mud pool, where most of them showed antibacterial activity. The genetic identification of most isolates was determined in BLASTn analyses of their 16S rRNA sequences. Isolates were identified as that of Streptomyces, Nocardia and Rhodococcus genus. Further, AntiSMASH results of the closest relatives of cultured actinobacteria have shown to produce antibiotics, natural pesticides and other compounds of various usage. This study also found no fecal coliforms and supports existing knowledge and practice of using Fijian thermal mud pools for their therapeutic properties. Overall, the presented work indicated that the studied mud pools have therapeutic properties, harboring wealth of bacteria with antibiotic profiles and were risk free from health-related issues of heavy metals and disease-causing pathogens. It provides great insight into the studied mud pools which serves as a baseline from which further heavy metal monitoring or mitigation programs and microbial researches can be conducted.

Insight into Different Stages of Steroid Degradation in Thermophilic Saccharopolyspora hirsuta VKM Ac-666T Strain

Steroids are abundant molecules in nature, and various microorganisms evolved to utilize steroids. Thermophilic actinobacteria play an important role in such processes. However, very few thermophiles have so far been reported capable of degrading or modifying natural sterols. Recently, genes putatively involved in the sterol catabolic pathway have been revealed in the moderately thermophilic actinobacterium Saccharopolyspora hirsuta VKM Ac-666^T, but peculiarities of strain activity toward sterols are still poorly understood. S. hirsuta catalyzed cholesterol bioconversion at a rate significantly inferior to that observed for mesophilic actinobacteria (mycobacteria and rhodococci). Several genes related to different stages of steroid catabolism increased their expression in response to cholesterol as was shown by transcriptomic studies and verified by RT-qPCR. Sequential activation of genes related to the initial step of cholesterol side chain oxidation (cyp125) and later steps of steroid core degradation (kstD3, kshA, ipdF, and fadE30) was demonstrated for the first time. The activation correlates with a low cholesterol conversion rate and intermediate accumulation by the strain. The transcriptomic analyses revealed that the genes involved in sterol catabolism are linked functionally, but not transcriptionally. The results contribute to the knowledge on steroid catabolism in thermophilic actinobacteria and could be used at the engineering of microbial catalysts.

Diversity, mechanisms and beneficial features of phosphate-solubilizing Streptomyces in sustainable agriculture: A review

Currently, the use of phosphate (P) biofertilizers among many bioformulations has attracted a large amount of interest for sustainable agriculture. By acting as growth promoters, members of the Streptomyces genus can positively interact with plants. Several studies have shown the great potential of this bacterial group in supplementing P in a soluble, plant-available form by several mechanisms. Furthermore, some P-solubilizing Streptomyces (PSS) species are known as plant growth-promoting rhizobacteria that are able to promote plant growth through other means, such as increasing the availability of soil nutrients and producing a wide range of antibiotics, phytohormones, bioactive compounds, and secondary metabolites other than antimicrobial compounds. Therefore, the use of PSS with multiple plant growth-promoting activities as an alternative strategy appears to limit the negative impacts of chemical fertilizers in agricultural practices on environmental and human health, and the potential effects of these PSS on enhancing plant fitness and crop yields have been explored. However, compared with studies on the use of other gram-positive bacteria, studies on the use of Streptomyces as P solubilizers are still lacking, and their results are unclear. Although PSS have been reported as potential bioinoculants in both greenhouse and field experiments, no PSS-based biofertilizers have been commercialized to date. In this regard, this review provides an overview mainly of the P solubilization activity of Streptomyces species, including their use as P biofertilizers in competitive agronomic practices and the mechanisms through which they release P by solubilization/mineralization, for both increasing P use efficiency in the soil and plant growth. This review further highlights and discusses the beneficial association of PSS with plants in detail with the latest developments and research to expand the knowledge concerning the use of PSS as P biofertilizers for field applications by exploiting their numerous advantages in improving crop production to meet global food demands.

New approach strategy for heavy metals immobilization and microbiome structure long-term industrially contaminated soils

The progress of engineering technologies highly influences the development of methods that lead to the condition improvement of areas contaminated with heavy metals (HMs). The aided phytostabilization fits into this trend, and was used to evaluate HM-immobilization effectiveness in phytostabilized soils under variable temperatures by applying 16 freezing-thawing cycles (FTC). Diatomite amendment and Lolium perenne L., also were applied. Cd/Ni/Cu/Pb/Zn each total content in phytostabilized soils were determined, along with the verification for each metal of its distribution in four extracted fractions (F1 ÷ F4) from soils. Based on changes in HM distribution, each metal's stability was estimated. Moreover, HM accumulation in plant roots and stems and soil microbial composition were investigated. Independently of the experimental variant (no-FTC-exposure or FTC-exposure), the above-ground biomass yields in the diatomite-amended series were higher as compared to the corresponding control series. The evident changes in Pb/Zn-bioavailability were observed. The metal stability increase was mainly attributed to metal concentration decreasing in the F1 fraction and increasing in the F4 fraction, respectively. Diatomite increased Cd/Zn-stability in not-FTC-exposed-phytostabilized soils. FTC-exposure favorably influenced Pb/Zn stability. Diatomite increased soil pH values and Cd/Ni/Cu/Zn-bioaccumulation (except Pb) in roots than in stems (in both experimental variants). FTC-exposure influenced soil microbial composition, increasing bacteria abundance belonging to Actinobacteria, Gammaproteobacteria, and Sphingobacteria. At the genus level, FTC exposure significantly increased the abundances of Limnobacter sp., Tetrasphaera sp., Flavobacterium sp., and Dyella sp. Independently of the experimental variant, Sphingomonas sp. and Mycobacterium sp., which have a tolerance to HM contamination, were core bacterial groups, comprising about 6 ÷ 7% of all soil bacteria.

Rootstock Priming with Shikimic Acid and Streptomyces griseus for Growth, Productivity, Physio-Biochemical, and Anatomical Characterisation of Tomato Grown under Cold Stress

With this research, we aimed to determine the impact of grafting and rootstock seed treated with Streptomyces griseus (MT210913) (S. griseus) or shikimic acid (SA) at a 60 ppm concentration on tomato (Solanum lycopersicum L.) production grown under low-temperature conditions. Two open-field trials were performed during both winter seasons of 2020 and 2021 at the Experimental Farm, Faculty of Agriculture, Cairo University, Giza, Egypt. A tomato cultivar (Peto 86) was used as a scion and two tomato phenotypes were employed as rootstocks (Solanum cheesmaniae L. (line LA 524) and GS hybrid), as well as self-grafted as a control. Effects of sub-optimal temperature on vegetative growth, yield, and fruit quality were tested. The results indicate that, under cold stress, rootstock seed priming, especially with S. griseus, enhanced plant growth, total yield, and fruit quality properties. GS hybrid rootstock was more effective than that of S. cheesmaniae rootstock in terms of mitigating the negative effect of cold stress. GS hybrid, inoculated with S. griseus, increased the total yield per plant by 10.5% and 5.7% in the first and second seasons, respectively. Higher levels of GA3 and mineral content were noticed in leaves that were grafted and treated with S. griseus compared to the control treatment. Additionally, the great enhancing effects of all anatomical features of tomato plants were recorded with GS hybrid rootstock, inoculated by S. griseus. These results prove that grafting on GS hybrid rootstock treated with S. griseus is a potential choice to alleviate the cold stress of commercial tomato varieties.

Microbial cooperation promotes humification to reduce antibiotic resistance genes abundance in food waste composting

Antibiotic resistance genes (ARGs) fate in a full-scale Food waste (FW) facility was investigated. Results showed that with the changes in ARGs, microbial networks could be naturally divided into two clusters, named as the ARGs increasing group (AI group) and the ARGs decreasing group (AD group). The significant difference between two groups (i.e. stronger microbial competition in the AI group and stronger microbial cooperation in the AD group) implied that the variation in ARGs over time were caused by a switch between competition and cooperation. These results indicated that microbial competition might increase ARGs abundance, while cooperation might reduce it. Meanwhile, structural-equation-model (SEM model) showed that humification indexes (e.g. GI value) was an indicator for characterizing microbial interactions and ARGs. The results of the linear model further confirmed that mature compost (GI values > 92.6 %) could reduce the risk of ARGs.

Core fungal species strengthen microbial cooperation in a food-waste composting process

In ecosystem engineering research, the contribution of microbial cooperation to ecosystem function has been emphasized. Fungi are one of the predominant decomposers in composting, but thus far, less attention has been given to fungal than to bacterial cooperation. Therefore, network and cohesion analyses were combined to reveal the correlation between fungal cooperation and organic matter (OM) degradation in ten composting piles. Positive cohesion, reflecting the cooperation degree, was positively linked to the degradation rate of OM. From the community perspective, core species (i.e., Candida tropicalis, Issatchenkia orientails, Kazachstania exigua, and Dipodascus australiensis) with high occurrence frequency and abundance were the key in regulating positive cohesion. These species were highly relevant to functional genera associated with OM degradation in both fungal and bacterial domains. Therefore, focusing on these core fungal species might be an appropriate strategy for targeted regulation of functional microbes and promotion of degradation rates.

Comparative Genome Analysis of a Novel Alkaliphilic Actinobacterial Species Nesterenkonia haasae

In the present study, a comparative genome analysis of the novel alkaliphilic actinobacterial Nesterenkonia haasae with other members of the genus Nesterenkonia was performed. The genome size of Nesterenkonia members ranged from 2,188,008 to 3,676,111 bp. N. haasae and Nesterenkonia members of the present study encode the essential glycolysis and pentose phosphate pathway genes. In addition, some Nesterenkonia members encode the crucial genes for Entner-Doudoroff pathways. Some Nesterenkonia members possess the genes responsible for sulfate/thiosulfate transport system permease protein/ ATP-binding protein and conversion of sulfate to sulfite. Nesterenkonia members also encode the genes for assimilatory nitrate reduction, nitrite reductase, and the urea cycle. All Nesterenkonia members have the genes to overcome environmental stress and produce secondary metabolites. The present study helps to understand N. haasae and Nesterenkonia members' environmental adaptation and niches specificity based on their specific metabolic properties. Further, based on genome analysis, we propose reclassifying Nesterenkonia jeotgali as a later heterotypic synonym of Nesterenkonia sandarakina.

A review on biosurfactant producing bacteria for remediation of petroleum contaminated soils

The discharge of potentially toxic petroleum hydrocarbons into the environment has been a matter of concern, as these organic pollutants accumulate in many ecosystems due to their hydrophobicity and low bioavailability. Petroleum hydrocarbons are neurotoxic and carcinogenic organic pollutants, extremely harmful to human and environmental health. Traditional treatment methods for removing hydrocarbons from polluted areas, including various mechanical and chemical strategies, are ineffective and costly. However, many indigenous microorganisms in soil and water can utilise hydrocarbon compounds as sources of carbon and energy and hence, can be employed to degrade hydrocarbon contaminants. Therefore, bioremediation using bacteria that degrade petroleum hydrocarbons is commonly viewed as an environmentally acceptable and effective method. The efficacy of bioremediation can be boosted further by using potential biosurfactant-producing microorganisms, as biosurfactants reduce surface tension, promote emulsification and micelle formation, making hydrocarbons bio-available for microbial breakdown. Further, introducing nanoparticles can improve the solubility of hydrophobic hydrocarbons as well as microbial synthesis of biosurfactants, hence establishing a favourable environment for microbial breakdown of these chemicals. The review provides insights into the role of microbes in the bioremediation of soils contaminated with petroleum hydrocarbons and emphasises the significance of biosurfactants and potential biosurfactant-producing bacteria. The review partly focusses on how nanotechnology is being employed in different critical bioremediation processes.

DETECTION OF ANTIMICROBIAL COMPOUNDS FROM THERMOPHILIC ACTINOMYCETES USING ONE STRAIN MANY COMPOUNDS (OSMAC) APPROACH

Actinomycetes are a group of filamentous bacteria with high biosynthetic potential that can produce secondary metabolites. Actinomycetes are known to produce secondary metabolites which are potential as antimicrobial, antitumor, and others. Actinomycetes can be found abundantly in diverse environments, including environments with extremely high temperatures such as hot springs, deserts, geothermal areas, and hydrothermal vents. They can survive in high temperatures due to their membrane lipids containing straight-chains and more saturated fatty acids that protect the membrane's fluidity to maintain membrane function. Thermophilic actinomycetes are potential producers of thermostable enzymes and bioactive compounds, which are important in the pharmaceutical, health, and industrial fields. Thermophilic actinomycetes are still less explored for novel metabolites and antimicrobial compounds due to the difficulty in isolation, maintenance, and preservation in pure culture. Novel bioactive compounds produced by actinomycetes are conventionally discovered by isolating potential strains and screening the compound bioactivity through various bioassays. A sequence-independent approach, termed the OSMAC (one strain many compounds), has been widely used in natural product research for activating cryptic biosynthetic gene clusters (BGCs) by modifying the growth conditions of a bacterial culture. This approach aims to optimize the number of secondary metabolites produced by one single microorganism. The application of the OSMAC method has been proven successful in revealing the biosynthetic potential of bacteria.

Biocontrol of Wilt disease of rice seedlings incited by Fusarium oxysporum through soil application of Streptomyces chilikensis RC1830

The genus Streptomyces includes many antifungal metabolite producing novel strains. Fusarium oxysporum a soil-inhabiting pathogenic fungi, that affects rice to cause wilt disease. This work demonstrates the efficacy of novel Streptomyces chilikensis strain RC1830, previously isolated from estuarine habitat Chilika Lake in preventing the F. oxysporum wilting/root rot disease and promoting the growth of rice (Var. Swarna) seedlings. A total of 25 different compounds were identified from crude extracts of S. chilikensis RC1830 by GC-MS. In pot trial experiments, Streptomyces treated rice seedlings showed significantly reduced Disease severity index (DSI) by 80.51%. The seedlings growth parameters (root length, root fresh weight and root dry weight )were also increased by 53.91%, 62.5%, 73.46% respectively in Streptomyces treated groups of seedlings compared to Fusarium infected seedlings. Similarly, the shoot length, shoot dry weight and shoot fresh weight were also increased by 26%, 58% and 34.4% respectively in Streptomyces treated groups of seedlings compared to Fusarium infected seedlings. Formulations of the strain were prepared using seven organic & inorganic wastes as the carrier material and the shelf lives of the propagules were also monitored. Vermiculite and activated charcoal formulations stored at 4°C exhibited a higher viable cell count after 3 months of storage.

Analysis of Bacterial Diversity in Different Types of Daqu and Fermented Grains From Danquan Distillery

Bacterial communities in high-temperature Daqu and fermented grains are important for brewing Jiang-flavor Baijiu such as Danquan Baijiu. Daqu is a saccharifying and fermenting agent, which has a significant impact on the flavor of Baijiu. However, bacterial communities in three different types of samples from the Danquan distillery (dqjq_ck, dqjqcp, and dqjp3) were still unclear, which limited further development of Danquan Baijiu. “dqjq_ck” and “dqjqcp” indicate high-temperature Daqu at days 45 and 135, respectively. “dqjp3” indicates fermented grains. In this study, the bacterial communities of three samples were analyzed by Illumina Miseq high-throughput sequencing. The bacterial communities of three samples primarily composed of thermophilic bacteria and bacteria with stress resistance. The most abundant species in dqjq_ck, dqjqcp, and dqjp3 were Comamonas, Bacillus, and unclassified Lactobacillales, respectively. The main bacteria included Bacillus, Comamonas, Myroides, Paenibacillus, Acetobacter, Kroppenstedtia, Staphylococcus, Saccharopolyspora, Planifilum, Lactobacillus, Acinetobacter, Oceanobacillus, Enterococcus, Thermoactinomyces, Lactococcus, Streptomyces, Saccharomonospora, Tepidimicrobium, Anaerosalibacter, unclassified_Lactobacillales, unclassified_Thermoactinomycetaceae_1, unclassified_Bacillaceae_2, unclassified_Bacillales, unclassified_Microbacteriaceae, unclassified_Rhodobacteraceae, unclassified_Actinopolysporineae, and unclassified_Flavobacteriaceae in three samples (percentage was more than 1% in one of three samples). In our study, the succession of microbiota in three samples representing three important stages of Danquan Baijiu brewing was revealed. This article lays a good foundation for understanding the fermentation mechanism and screening some excellent indigenous bacteria to improve the quality of Danquan Baijiu in future.

Management Practices Affecting Lesser Mealworm Larvae (Alphitobius diaperinus) Associated Microbial Community in a Broiler House and After Relocating With the Litter Into Pastureland

Lesser mealworms are often found infesting production houses used to raise broiler chickens. Previous studies have investigated pathogenic microorganisms associated with the larvae, but a more thorough study relating total microbiome changes due to management procedures and flock rotations was needed. Additionally, there is a question of what microbiota are transferred into the environment when the litter, in which larvae reside, is piled in pastureland for use as fertilizer and where interactions with the soil and other fauna can occur. This study chronicled, by the 16S rRNA sequencing, the bacterial community profile of larvae in a broiler grow-out house synchronizing to when birds were added to and removed from the house over 2.5 years. The profile was found to be relatively constant despite 11 flock rotations and management disruptions, specifically litter cleanout procedures and the addition of new birds or bedding. In contrast, once removed from the controlled broiler house environment and placed into open pastureland, the substantial microbial diversity brought with the larvae showed greater fluctuation in structure with environmental conditions, one of which was rainfall. Surprisingly, these larvae survived at least 19 weeks, so the potential for moving larval-associated microbes into the environment needs further assessment to minimize the risk of relocating foodborne pathogens and also to assess those bacteria-generating metabolites that have benefits to plant growth when using the litter as a fertilizer. The characterization of their microbiome is the first step to investigating the influences of their microbes on the manmade and environmental ecosystems.

Streptomyces: Still the Biggest Producer of New Natural Secondary Metabolites, a Current Perspective

There is a real consensus that new antibiotics are urgently needed and are the best chance for combating antibiotic resistance. The phylum Actinobacteria is one of the main producers of new antibiotics, with a recent paradigm shift whereby rare actinomycetes have been increasingly targeted as a source of new secondary metabolites for the discovery of new antibiotics. However, this review shows that the genus Streptomyces is still the largest current producer of new and innovative secondary metabolites. Between January 2015 and December 2020, a significantly high number of novel Streptomyces spp. have been isolated from different environments, including extreme environments, symbionts, terrestrial soils, sediments and also from marine environments, mainly from marine invertebrates and marine sediments. This review highlights 135 new species of Streptomyces during this 6-year period with 108 new species of Streptomyces from the terrestrial environment and 27 new species from marine sources. A brief summary of the different pre-treatment methods used for the successful isolation of some of the new species of Streptomyces is also discussed, as well as the biological activities of the isolated secondary metabolites. A total of 279 new secondary metabolites have been recorded from 121 species of Streptomyces which exhibit diverse biological activity. The greatest number of new secondary metabolites originated from the terrestrial-sourced Streptomyces spp.

A Review on Biotechnological Approaches Applied for Marine Hydrocarbon Spills Remediation

The increasing demand for petroleum products generates needs for innovative and reliable methods for cleaning up crude oil spills. Annually, several oil spills occur around the world, which brings numerous ecological and environmental disasters on the surface of deep seawaters like oceans. Biological and physico-chemical remediation technologies can be efficient in terms of spill cleanup and microorganisms—mainly bacteria—are the main ones responsible for petroleum hydrocarbons (PHCs) degradation such as crude oil. Currently, biodegradation is considered as one of the most sustainable and efficient techniques for the removal of PHCs. However, environmental factors associated with the functioning and performance of microorganisms involved in hydrocarbon-degradation have remained relatively unclear. This has limited our understanding on how to select and inoculate microorganisms within technologies of cleaning and to optimize physico-chemical remediation and degradation methods. This review article presents the latest discoveries in bioremediation techniques such as biostimulation, bioaugmentation, and biosurfactants as well as immobilization strategies for increasing the efficiency. Besides, environmental affecting factors and microbial strains engaged in bioremediation and biodegradation of PHCs in marines are discussed.

Moroccan Lagoon Microbiomes

Lagoons are fragile marine ecosystems that are considerably affected by anthropogenic pollutants. We performed a spatiotemporal characterization of the microbiome of two Moroccan lagoons, Marchica and Oualidia, both classified as Ramsar sites, the former on the Mediterranean coast and the latter on the Atlantic coast. We investigated their microbial diversity and abundance using 16S rRNA amplicon- and shotgun-based metagenomics approaches during the summers of 2014 and 2015. The bacterial microbiome was composed primarily of Proteobacteria (25–53%, 29–29%), Cyanobacteria (34–12%, 11–0.53%), Bacteroidetes (24–16%, 23–43%), Actinobacteria (7–11%, 13–7%), and Verrucomicrobia (4–1%, 15–14%) in Marchica and Oualidia in 2014 and 2015, respectively. Interestingly, 48 strains were newly reported in lagoon ecosystems, while eight unknown viruses were detected in Mediterranean Marchica only. Statistical analysis showed higher microbial diversity in the Atlantic lagoon than in the Mediterranean lagoon and a robust relationship between alpha diversity and geographic sampling locations. This first-ever metagenomics study on Moroccan aquatic ecosystems enriched the national catalog of marine microorganisms. They will be investigated as candidates for bioindication properties, biomonitoring potential, biotechnology valorization, biodiversity protection, and lagoon health assessment.

Effect of Biochar on Metal Distribution and Microbiome Dynamic of a Phytostabilized Metalloid-Contaminated Soil Following Freeze-Thaw Cycles

In the present paper the effectiveness of biochar-aided phytostabilization of metal/metalloid-contaminated soil under freezing-thawing conditions and using the metal tolerating test plant Lolium perenne L. is comprehensively studied. The vegetative experiment consisted of plants cultivated for over 52 days with no exposure to freezing-thawing in a glass greenhouse, followed by 64 days under freezing-thawing in a temperature-controlled apparatus and was carried out in initial soil derived from a post-industrial urban area, characterized by the higher total content of Zn, Pb, Cu, Cr, As and Hg than the limit values included in the classification provided by the Regulation of the Polish Ministry of Environment. According to the substance priority list published by the Toxic Substances and Disease Registry Agency, As, Pb, and Hg are also indicated as being among the top three most hazardous substances. The initial soil was modified by biochar obtained from willow chips. The freeze-thaw effect on the total content of metals/metalloids (metal(-loid)s) in plant materials (roots and above-ground parts) and in phytostabilized soils (non- and biochar-amended) as well as on metal(-loid) concentration distribution/redistribution between four BCR (community bureau of reference) fractions extracted from phytostabilized soils was determined. Based on metal(-loid)s redistribution in phytostabilized soils, their stability was evaluated using the reduced partition index (Ir). Special attention was paid to investigating soil microbial composition. In both cases, before and after freezing-thawing, biochar increased plant biomass, soil pH value, and metal(-loid)s accumulation in roots, and decreased metal(-loid)s accumulation in stems and total content in the soil, respectively, as compared to the corresponding non-amended series (before and after freezing-thawing, respectively). In particular, in the phytostabilized biochar-amended series after freezing-thawing, the recorded total content of Zn, Cu, Pb, and As in roots substantially increased as well as the Hg, Cu, Cr, and Zn in the soil was significantly reduced as compared to the corresponding non-amended series after freezing-thawing. Moreover, exposure to freezing-thawing itself caused redistribution of examined metal(-loid)s from mobile and/or potentially mobile into the most stable fraction, but this transformation was favored by biochar presence, especially for Cu, Pb, Cr, and Hg. While freezing-thawing greatly affected soil microbiome composition, biochar reduced the freeze-thaw adverse effect on bacterial diversity and helped preserve bacterial groups important for efficient soil nutrient conversion. In biochar-amended soil exposed to freezing-thawing, psychrotolerant and trace element-resistant genera such as Rhodococcus sp. or Williamsia sp. were most abundant.

Microbial interaction promote the degradation rate of organic matter in thermophilic period

Composting is an efficient, microbe-driven method for the biodegradation of solid organic substrates. In such a complex engineering ecosystem, microbial interaction is more important to function than relative abundance and alpha diversity. However, microbial interaction and its driving force in the composting process has been rarely reported. Thus, we combined network analysis and positive cohesion to analyze the relationship between cooperation among bacteria taxa and the degradation of organic matter in ten industrial-scale food waste composting piles. The results showed that although the complexity of network and microbial diversity were inhibited by high temperature, microbial cooperation was stimulated in the thermophilic period. The positive cohesion, which reflected the degree of microbial cooperation, tended to be positively correlated with the degradation rate of organic matter, functional genera, and genes associated with organic matter degradation. Thus, microbial cooperation was a key factor in the promotion of the degradation of organic matter. From the insight microbial community, Thermobifida was the genera with high abundance, high occurrence frequency, and high contributions to microbial structure. Additionally, it was not only highly associated with the degree of cooperation but was also highly linked with the functional genera in the composting, implying that it might play an important role in regulating cooperation to promote the functional genera. Our research provides a deep understanding of the interaction among bacteria taxa during the composting process. Focusing on the abundance of Thermobifida might be an efficient way to improve composting quality by enhancing the cooperation of microbes.

Physico-Chemical and Metagenomic Profile Analyses of Animal Manures Routinely Used as Inocula in Anaerobic Digestion for Biogas Production

Anaerobic digestion (AD) of organic waste is considered a sustainable solution to energy shortage and waste management challenges. The process is facilitated by complex communities of micro-organisms, yet most wastes do not have these and thus need microbial inoculation using animal manures to initiate the process. However, the degradation efficiency and methane yield achieved in using different inocula vary due to their different microbial diversities. This study used metagenomics tools to compare the autochthonous microbial composition of cow, pig, chicken, and horse manures commonly used for biogas production. Cows exhibited the highest carbon utilisation (>30%) and showed a carbon to nitrogen ratio (C/N) favourable for microbial growth. Pigs showed the least nitrogen utilisation (<3%) which explains their low C/N whilst horses showed the highest nitrogen utilisation (>40%), which explains its high C/N above the optimal range of 20−30 for efficient AD. Manures from animals with similar gastrointestinal tract (GIT) physiologies were observed to largely harbour similar microbial communities. Conversely, some samples from animals with different GITs also shared common microbial communities plausibly because of similar diets and rearing conditions. Insights from this study will lay a foundation upon which in-depth studies of AD metabolic pathways and strategies to boost methane production through efficient catalysis can be derived.

Actinomycetes from Caves: An Overview of Their Diversity, Biotechnological Properties, and Insights for Their Use in Soil Environments

The environmental conditions of caves shape microbiota. Within caves' microbial communities, actinomycetes are among the most abundant bacteria. Cave actinomycetes have gained increasing attention during the last decades due to novel bioactive compounds with antibacterial, antioxidant and anticancer activities. However, their potential role in soil environments is still unknown. This review summarises the literature dealing with actinomycetes from caves, underlining for the first time their potential roles in soil environments. We provide an overview of their diversity and biotechnological properties, underling their potential role in soil environments applications. The contribution of caves' actinomycetes in soil fertility and bioremediation and crops biostimulation and biocontrol are discussed. The survey on the literature show that several actinomycetes genera are present in cave ecosystems, mainly Streptomyces, Micromonospora, and Nocardiopsis. Among caves' actinomycetes, Streptomyces is the most studied genus due to its ubiquity, survival capabilities, and metabolic versatility. Despite actinomycetes' outstanding capabilities and versatility, we still have inadequate information regarding cave actinomycetes distribution, population dynamics, biogeochemical processes, and metabolisms. Research on cave actinomycetes needs to be encouraged, especially concerning environmental soil applications to improve soil fertility and health and to antagonise phytopathogens.

Synthetic Biology of Thermophiles: Taking Bioengineering to the Extremes?

Synthetic biology applications rely on a well-characterized set of microbial strains, with an established toolbox of molecular biology methods for their genetic manipulation. Since there are no thermophiles with such attributes, most biotechnology and synthetic biology studies use organisms that grow in the mesophilic temperature range. As a result, thermophiles, a heterogenous group of microbes that thrive at high (>50 °C) temperatures, are largely overlooked, with respect to their biotechnological potential, even though they share several favorable traits. Thermophilic bacteria tend to grow at higher rates compared to their mesophilic counterparts, while their growth has lower cooling requirements and is less prone to contamination. Over the last few years, there has been renewed interest in developing tools and methods for thermophile bioengineering. In this perspective, we explain why it is a good idea to invest time and effort into developing a thermophilic synthetic biology direction, which is the state of the art, and why we think that the implementation of a thermophilic synthetic biology platform—a thermochassis—will take synthetic biology to the extremes.

Leveraging multiomics approaches for producing lignocellulose degrading enzymes

Lignocellulosic materials form the building block of 50% of plant biomass comprising non-chewable agri-components like wheat straw, rice stubbles, wood shavings and other crop residues. The degradation of lignin, cellulose and hemicellulose is complicated and presently being done by chemical process for industrial application through a very energy intensive process. Lignin degradation is primarily an oxidative process where the enzyme lignin peroxidase digests the polymer into smaller fragments. Being a recalcitrant component, higher lignin content poses a challenge of lower recovery of product for industrial use. Globally, the scientists are working on leveraging fungal biotechnology for using the lignocellulose degrading enzymes secreted by actinomycetes and basidiomycetes fungal groups. Enzymes contributing to degradation of lignin are mainly performing the function of modifying the lignin and degrading the lignin. Ligninolytic enzymes do not act as an independent reaction but are vital to complete the degradation process. Microbial enzyme technology is an emerging green tool in industrial biotechnology for commercial application. Bioprocessing of lignocellulosic biomass is challenged by limitations in enzymatic and conversion process where pretreatment and separation steps are done to remove lignin and hydrolyze carbohydrate into fermentable sugars. This review highlights recent advances in molecular biotechnology, lignin valorization, sequencing, decipher microbial membership, and characterize enzyme diversity through 'omics' techniques. Emerging techniques to characterize the interwoven metabolism and spatial interactions between anaerobes are also reviewed, which will prove critical to developing a predictive understanding of anaerobic communities to guide in microbiome engineering This requires more synergistic collaborations from microbial biotechnologists, bioprocess engineers, enzymologists, and other biotechnological fields.

Roots of the xerophyte Panicum turgidum host a cohort of ionizing-radiation-resistant biotechnologically-valuable bacteria

Bacterial communities associated with roots of Panicum turgidum, exposed to arid conditions, were investigated with a combination of cultural and metataxonomic approaches. Traditional culture-based techniques were used and 32 isolates from the irradiated roots were identified as belonging to Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria phyla. Four actinobacterial strains were shown to be ionizing-radiation (IR)-resistant: Microbacterium sp. PT8 (4.8 kGy (kGy)), Micrococcus sp. PT11 (4.4 kGy), Kocuria rhizophila PT10 (2.9 kGy) and Promicromonospora panici PT9^T (2.6 kGy), based on the D₁₀ dose necessary for a 90% reduction in colony forming units (CFU). Concerning the investigation of microbial communities in situ, metataxonomic analyses of the diversity of IR-resistant microorganisms associated with irradiated roots revealed a marked dominance of Actinobacteria (46.6%) and Proteobacteria (31.5%) compared to Bacteroidetes (4.6%) and Firmicutes (3.2%). Gamma irradiation not only changed the structure of bacterial communities, but also affected their functional properties. Comparative analyses of metabolic profiles indicated the induction of several pathways related to adaptation to oxidative stress in irradiated roots, such as DNA repair, secondary metabolites synthesis, reactive oxygen species (ROS)-mitigating enzymes, etc. P. turgidum is emblematic of desert-adapted plants. Until now, there is no other work that has focused on the microbial profile of irradiated roots of this xerophyte.

Kocuria Strains from Unique Radon Spring Water from Jachymov Spa

Members of the genus Kocuria are often found in soils contaminated with toxic metals or exposed to high levels of ionizing radiation. The use of classical cultivation technics often leads to the isolation of Kocuria sp. from underground spring waters. These bacterial isolates have to adapt their metabolism to survive in such extreme environments. Four bacterial isolates of the genus Kocuria (Kocuria sp. 101, 208, 301, and 401) were obtained from radon spring water (Jachymov, Czech Republic). These isolates were tested for their ability to withstand stress and extreme conditions. Growth was observed at a temperature range of 10–45 °C with optimal growth temperature between 20 and 30 °C. The content of polyunsaturated fatty acids in all four isolates was proved to be temperature-dependent. The strain Kocuria sp. 301 showed high resistance to all studied extreme conditions (UV radiation, desiccation, and free radicals in medium). The results suggest that isolates from radioactive springs might have developed mechanisms that help them survive under several extreme conditions and could be used in biotechnological production.

Steroid Metabolism in Thermophilic Actinobacterium Saccharopolyspora hirsuta VKM Ac-666T

The application of thermophilic microorganisms opens new prospects in steroid biotechnology, but little is known to date on steroid catabolism by thermophilic strains. The thermophilic strain Saccharopolyspora hirsuta VKM Ac-666^T has been shown to convert various steroids and to fully degrade cholesterol. Cholest-4-en-3-one, cholesta-1,4-dien-3-one, 26-hydroxycholest-4-en-3-one, 3-oxo-cholest-4-en-26-oic acid, 3-oxo-cholesta-1,4-dien-26-oic acid, 26-hydroxycholesterol, 3β-hydroxy-cholest-5-en-26-oic acid were identified as intermediates in cholesterol oxidation. The structures were confirmed by ¹H and ¹³C-NMR analyses. Aliphatic side chain hydroxylation at C26 and the A-ring modification at C3, which are putatively catalyzed by cytochrome P450 monooxygenase CYP125 and cholesterol oxidase, respectively, occur simultaneously in the strain and are followed by cascade reactions of aliphatic sidechain degradation and steroid core destruction via the known 9(10)-seco-pathway. The genes putatively related to the sterol and bile acid degradation pathways form three major clusters in the S. hirsuta genome. The sets of the genes include the orthologs of those involved in steroid catabolism in Mycobacterium tuberculosis H37Rv and Rhodococcus jostii RHA1 and related actinobacteria. Bioinformatics analysis of 52 publicly available genomes of thermophilic bacteria revealed only seven candidate strains that possess the key genes related to the 9(10)-seco pathway of steroid degradation, thus demonstrating that the ability to degrade steroids is not widespread among thermophilic bacteria.