Tapping into microbial diversity

Important soil microbiota's effects on plants and soils: a comprehensive 30-year systematic literature review

Clarifying the relationship between soil microorganisms and the plant-soil system is crucial for encouraging the sustainable development of ecosystems, as soil microorganisms serve a variety of functional roles in the plant-soil system. In this work, the influence mechanisms of significant soil microbial groups on the plant-soil system and their applications in environmental remediation over the previous 30 years were reviewed using a systematic literature review (SLR) methodology. The findings demonstrated that: (1) There has been a general upward trend in the number of publications on significant microorganisms, including bacteria, fungi, and archaea. (2) Bacteria and fungi influence soil development and plant growth through organic matter decomposition, nitrogen, phosphorus, and potassium element dissolution, symbiotic relationships, plant growth hormone production, pathogen inhibition, and plant resistance induction. Archaea aid in the growth of plants by breaking down low-molecular-weight organic matter, participating in element cycles, producing plant growth hormones, and suppressing infections. (3) Microorganism principles are utilized in soil remediation, biofertilizer production, denitrification, and phosphorus removal, effectively reducing environmental pollution, preventing soil pathogen invasion, protecting vegetation health, and promoting plant growth. The three important microbial groups collectively regulate the plant-soil ecosystem and help maintain its relative stability. This work systematically summarizes the principles of important microbial groups influence plant-soil systems, providing a theoretical reference for how to control soil microbes in order to restore damaged ecosystems and enhance ecosystem resilience in the future.

Rhizobacterial syntrophy between a helper and a beneficiary promotes tomato plant health

Microbial interactions impact the functioning of microbial communities. However, microbial interactions within host-associated communities remain poorly understood. Here, we report that the beneficiary rhizobacterium Niallia sp. RD1 requires the helper Pseudomonas putida H3 for bacterial growth and beneficial interactions with the plant host. In the absence of the helper H3 strain, the Niallia sp. RD1 strain exhibited weak respiration and elongated cell morphology without forming bacterial colonies. A transposon mutant of H3 in a gene encoding succinate-semialdehyde dehydrogenase displayed much attenuated support of RD1 colony formation. Through the subsequent addition of succinate to the media, we found that succinate serves as a public good that supports RD1 growth. Comparative genome analysis highlighted that RD1 lacked the gene for sufficient succinate, suggesting its evolution as a beneficiary of succinate biosynthesis. The syntrophic interaction between RD1 and H3 efficiently protected tomato plants from bacterial wilt and promoted tomato growth. The addition of succinate to the medium restored complex II-dependent respiration in RD1 and facilitated the cultivation of various bacterial isolates from the rhizosphere. Taken together, we delineate energy auxotrophic beneficiaries ubiquitous in the microbial community, and these beneficiaries could benefit host plants with the aid of helpers in the rhizosphere.

The respiratory microbiota and its impact on health and disease in dogs and cats: A One Health perspective

Healthy lungs were long thought of as sterile, with presence of bacteria identified by culture representing contamination. Recent advances in metagenomics have refuted this belief by detecting rich, diverse, and complex microbial communities in the healthy lower airways of many species, albeit at low concentrations. Although research has only begun to investigate causality and potential mechanisms, alterations in these microbial communities (known as dysbiosis) have been described in association with inflammatory, infectious, and neoplastic respiratory diseases in humans. Similar studies in dogs and cats are scarce. The microbial communities in the respiratory tract are linked to distant microbial communities such as in the gut (ie, the gut-lung axis), allowing interplay of microbes and microbial products in health and disease. This review summarizes considerations for studying local microbial communities, key features of the respiratory microbiota and its role in the gut-lung axis, current understanding of the healthy respiratory microbiota, and examples of dysbiosis in selected respiratory diseases of dogs and cats.

The media composition as a crucial element in high-throughput metabolic network reconstruction

In recent years, metagenome-assembled genomes (MAGs) have provided glimpses into the intra- and interspecies genetic diversity and interactions that form the bases of complex microbial communities. High-throughput reconstruction of genome-scale metabolic networks (GEMs) from MAGs is a promising avenue to disentangle the myriad trophic interactions stabilizing these communities. However, high-throughput reconstruction of GEMs relies on accurate gap filling of metabolic pathways using automated algorithms. Here, we systematically explore how the composition of the media (specification of the available nutrients and metabolites) during gap filling influences the resulting GEMs concerning predicted auxotrophies for fully sequenced model organisms and environmental isolates. We expand this analysis by using 106 MAGs from the same species with differing quality. We find that although the completeness of MAGs influences the fraction of gap-filled reactions, the composition of the media plays the dominant role in the accurate prediction of auxotrophies that form the basis of myriad community interactions. We propose that constraining the media composition for gap filling through both experimental approaches and computational approaches will increase the reliability of high-throughput reconstruction of genome-scale metabolic models from MAGs and paves the way for culture independent prediction of trophic interactions in complex microbial communities.

Assessment of diversity of archaeal communities in Algerian chott

Halophilic archaea are the dominant type of microorganisms in hypersaline environments. The diversity of halophilic archaea in Zehrez-Chergui (Saharian chott) was analyzed and compared by both analysis of a library of PCR amplified 16S rRNA genes and by cultivation approach. This work, represents the first of its type in Algeria. A total cell count was estimated at 3.8 × 10³ CFU/g. The morphological, biochemical, and physiological characterizations of 45 distinct strains, suggests that all of them might be members of the class Halobacteria. Among stains, 23 were characterized phylogenetically and are related to 6 genera of halophilic archaea.The dominance of the genus Halopiger, has not been reported yet in other hypersaline environments. The 100 clones obtained by the molecular approach, were sequenced, and analyzed. The ribosomal library of 61 OTUs showed that the archaeal diversity included uncultured haloarcheon, Halomicrobium, Natronomonas, Halomicroarcula, Halapricum, Haloarcula, Halosimplex, Haloterrigena, Halolamina, Halorubellus, Halorussus and Halonotius. The results of rarefaction analysis indicated that the analysis of an increasing number of clones would have revealed additional diversity. Surprisingly, no halophilic archaea were not shared between the two approaches. Combining both types of methods was considered the best approach to acquire better information on the characteristics of soil halophilic archaea.

The selection of copiotrophs may complicate biodiversity-ecosystem functioning relationships in microbial dilution-to-extinction experiments

The relationships between biodiversity-ecosystem functioning (BEF) for microbial communities are poorly understood despite the important roles of microbes acting in natural ecosystems. Dilution-to-extinction (DTE), a method to manipulate microbial diversity, helps to fill the knowledge gap of microbial BEF relationships and has recently become more popular with the development of high-throughput sequencing techniques. However, the pattern of community assembly processes in DTE experiments is less explored and blocks our further understanding of BEF relationships in DTE studies. Here, a microcosm study and a meta-analysis of DTE studies were carried out to explore the dominant community assembly processes and their potential effect on exploring BEF relationships. While stochastic processes were dominant at low dilution levels due to the high number of rare species, the deterministic processes became stronger at a higher dilution level because the microbial copiotrophs were selected during the regrowth phase and rare species were lost. From the view of microbial functional performances, specialized functions, commonly carried by rare species, are more likely to be impaired in DTE experiments while the broad functions seem to be less impacted due to the good performance of copiotrophs. Our study indicated that shifts in the prokaryotic community and its assembly processes induced by dilutions result in more complex BEF relationships in DTE experiments. Specialized microbial functions could be better used for defining BEF. Our findings may be helpful for future studies to design, explore, and interpret microbial BEF relationships using DTE.

Bovine neonatal microbiome origins: a review of proposed microbial community presence from conception to colostrum

In recent years, there has been an influx of research evaluating the roles of the reproductive tract microbiota in modulating reproductive performance. These efforts have resulted in a breadth of research exploring the bovine reproductive tract microbiota. The female reproductive tract microbiota has been characterized during the estrus cycle, at timed artificial insemination, during gestation, and postpartum. Additionally, there are recently published studies investigating in-utero inoculation of the bovine fetus. However, critical review of the literature to understand how the microbial shifts during a dam's lifecycle could impact neonatal outcomes is limited. This review demonstrates a consistency at the phyla level throughout both the maternal, paternal, and neonatal microbiomes. Moreover, this review challenges the current gestational inoculation hypothesis and suggests instead a maturation of the resident uterine microbiota throughout gestation to parturition. Recent literature is indicative of microbial composition influencing metabolomic parameters that have developmental programming effects in feed utilization and metabolic performance later in life. Thus, this review enumerates the potential origins of neonatal microbial inoculation from conception, through gestation, parturition, and colostrum consumption while introducing clear paucities where future research is needed to better understand the ramifications of the reproductive microbiome on neonates.

Exploring microbial functional biodiversity at the protein family level-From metagenomic sequence reads to annotated protein clusters

Metagenomics has enabled accessing the genetic repertoire of natural microbial communities. Metagenome shotgun sequencing has become the method of choice for studying and classifying microorganisms from various environments. To this end, several methods have been developed to process and analyze the sequence data from raw reads to end-products such as predicted protein sequences or families. In this article, we provide a thorough review to simplify such processes and discuss the alternative methodologies that can be followed in order to explore biodiversity at the protein family level. We provide details for analysis tools and we comment on their scalability as well as their advantages and disadvantages. Finally, we report the available data repositories and recommend various approaches for protein family annotation related to phylogenetic distribution, structure prediction and metadata enrichment.

Antibiotic Resistance of Selected Bacteria after Treatment of the Supragingival Biofilm with Subinhibitory Chlorhexidine Concentrations

Due to increasing rates of antibiotic resistance and very few novel developments of antibiotics, it is crucial to understand the mechanisms of resistance development. The aim of the present study was to investigate the adaptation of oral bacteria to the frequently used oral antiseptic chlorhexidine digluconate (CHX) and potential cross-adaptation to antibiotics after repeated exposure of supragingival plaque samples to subinhibitory concentrations of CHX. Plaque samples from six healthy donors were passaged for 10 days in subinhibitory concentrations of CHX, while passaging of plaque samples without CHX served as control. The surviving bacteria were cultured on agar plates and identified with Matrix-assisted Laser Desorption/Ionization-Time of Flight-Mass spectrometry (MALDI-TOF). Subsequently, the minimum inhibitory concentrations (MIC) of these isolates toward CHX were determined using a broth-microdilution method, and phenotypic antibiotic resistance was evaluated using the epsilometertest. Furthermore, biofilm-forming capacities were determined. Repeated exposure of supragingival plaque samples to subinhibitory concentrations of CHX led to the selection of oral bacteria with 2-fold up to 4-fold increased MICs toward CHX. Furthermore, these isolates showed up to 12-fold increased MICs towards some antibiotics such as erythromycin and clindamycin. Conversely, biofilm-forming capacity was decreased. In summary, this study shows that oral bacteria are able to adapt to CHX, while also decreasing their susceptibility to antibiotics.

Cultivating marine bacteria under laboratory conditions: Overcoming the “unculturable” dogma

Underexplored seawater environments may contain biological resources with potential for new biotechnological applications. Metagenomic techniques revolutionized the study of bacterial communities but culture dependent methods will still be important to help the biodiscovery of new products and enzymes from marine bacteria. In this context, we promoted the growth of bacteria from a marine rock pond by culture dependent techniques and compared the results with culture independent methods. The total number of bacteria and diversity were studied in different agar plate media during 6 weeks. Agar plate counting was of the same order of magnitude of direct microscopy counts. The highest efficiency of cultivation was 45% attained in marine agar medium. Molecular analysis revealed 10 different phyla of which only four were isolated by the culture dependent method. On the other hand, four taxonomic orders were detected by cultivation but not by the molecular technique. These include bacteria from the phyla Bacillota and Actinomycetota. Our study shows that it is possible to grow more than the traditionally considered 1% of bacteria from a seawater sample using standard agar plate techniques and laboratorial conditions. The results also demonstrate the importance of culture methods to grow bacteria not detected by molecular approaches for future biotechnological applications.

Induction of Diverse Cryptic Fungal Metabolites by Steroids and Channel Blockers

Fungi offer a deep source of natural products but remain underutilized. Most biosynthetic gene clusters (BGCs) that can be detected are silent or "cryptic" in standard lab cultures and their products are thus not interrogated in routine screens. As genetic alterations are difficult and some strains can only be grown on agar, we have herein applied an agar-based high-throughput chemical genetic screen to identify inducers of fungal BGCs. Using R. solani and S. sclerotiorum as test cases, we report 13 cryptic metabolites in four compound groups, including sclerocyclane, a natural product with a novel scaffold. Steroids were the best elicitors and follow-up studies showed that plant-steroids trigger sclerocyclane synthesis, which shows antibiotic activity against B. plantarii, an ecological competitor of S. sclerotiorum. Our results open new paths to exploring the chemical ecology of fungal-plant interactions and provide a genetics-free approach for uncovering cryptic fungal metabolites.

Biophilic Experience-Based Residential Hybrid Framework

There has been increasing academic interest in biophilic design in response to recent environmental and climate change issues, including the COVID-19 pandemic. However, discussions of the utilization of digital technology in providing universal access to nature, and opportunities to experience more diverse nature, are lacking. This study aimed to compare and analyze major theoretical systems for biophilic experiences in a residential environment, and to propose a hybrid framework that combines physical and digital design techniques for comparison and analysis. This paper discusses framework application strategies in line with scales of residential environments. Based on a systematic literature review, this study integrated and derived key elements of biophilic experience for a better quality of life in a modern residential environment and proposed a hybrid framework and strategy based on this. As a result, a hybrid framework of 15 integrated factors for three biophilic experiences was derived, and various strengths and potential opportunities were identified in terms of application depending on the scales. At the unit scale, it was found that the well-being and health of residents improved; at the building scale, the potential for sustainability was highlighted; at the complex scale, there was a contribution to higher residential competitiveness in multi-dimensional aspects. In particular, the biophilic experience-based hybrid framework in this study provided insights into addressing the weaknesses and threats discussed in the existing biophilic design.

Combination of high-throughput microfluidics and FACS technologies to leverage the numbers game in natural product discovery

High-throughput platforms facilitating screening campaigns of environmental samples are needed to discover new products of natural origin counteracting the spreading of antimicrobial resistances constantly threatening human and agricultural health. We applied a combination of droplet microfluidics and fluorescence-activated cell sorting (FACS)-based technologies to access and assess a microbial environmental sample. The cultivation performance of our microfluidics workflow was evaluated in respect to the utilized cultivation media by Illumina amplicon sequencing of a pool of millions of droplets, respectively. This enabled the rational selection of a growth medium supporting the isolation of microbial diversity from soil (five phyla affiliated to 57 genera) including a member of the acidobacterial subgroup 1 (genus Edaphobacter). In a second phase, the entire diversity covered by 1071 cultures was used for an arrayed bioprospecting campaign, resulting in > 6000 extracts tested against human pathogens and agricultural pests. After redundancy curation by using a combinatorial chemical and genomic fingerprinting approach, we assigned the causative agents present in the extracts. Utilizing UHPLC-QTOF-MS/MS-guided fractionation and microplate-based screening assays in combination with molecular networking the production of bioactive ionophorous macrotetrolides, phospholipids, the cyclic lipopetides massetolides E, F, H and serratamolide A and many derivatives thereof was shown.

A critical analysis of research methods and experimental models to study the root canal microbiome

Endodontic microbiology deals with the study of the microbial aetiology and pathogenesis of pulpal and periradicular inflammatory diseases. Research in endodontic microbiology started almost 130 years ago and since then has mostly focussed on establishing and confirming the infectious aetiology of apical periodontitis, identifying the microbial species associated with the different types of endodontic infections and determining the efficacy of treatment procedures in eradicating or controlling infection. Diverse analytical methods have been used over the years, each one with their own advantages and limitations. In this review, the main features and applications of the most used technologies are discussed, and advice is provided to improve study designs in order to properly address the scientific questions and avoid setbacks that can compromise the results. Finally, areas of future research are described.

MetFish: a Metabolomics Pipeline for Studying Microbial Communities in Chemically Extreme Environments

Metabolites have essential roles in microbial communities, including as mediators of nutrient and energy exchange, cell-to-cell communication, and antibiosis. However, detecting and quantifying metabolites and other chemicals in samples having extremes in salt or mineral content using liquid chromatography-mass spectrometry (LC-MS)-based methods remains a significant challenge. Here, we report a facile method based on in situ chemical derivatization followed by extraction for analysis of metabolites and other chemicals in hypersaline samples, enabling for the first time direct LC-MS-based exometabolomics analysis in sample matrices containing up to 2 M total dissolved salts. The method, MetFish, is applicable to molecules containing amine, carboxylic acid, carbonyl, or hydroxyl functional groups, and it can be integrated into either targeted or untargeted analysis pipelines. In targeted analyses, MetFish provided limits of quantification as low as 1 nM, broad linear dynamic ranges (up to 5 to 6 orders of magnitude) with excellent linearity, and low median interday reproducibility (e.g., 2.6%). MetFish was successfully applied in targeted and untargeted exometabolomics analyses of microbial consortia, quantifying amino acid dynamics in the exometabolome during community succession; in situ in a native prairie soil, whose exometabolome was isolated using a hypersaline extraction; and in input and produced fluids from a hydraulically fractured well, identifying dramatic changes in the exometabolome over time in the well.

IMPORTANCE The identification and accurate quantification of metabolites using electrospray ionization-mass spectrometry (ESI-MS) in hypersaline samples is a challenge due to matrix effects. Clean-up and desalting strategies that typically work well for samples with lower salt concentrations are often ineffective in hypersaline samples. To address this gap, we developed and demonstrated a simple yet sensitive and accurate method—MetFish—using chemical derivatization to enable mass spectrometry-based metabolomics in a variety of hypersaline samples from varied ecosystems and containing up to 2 M dissolved salts.

Triggering Growth via Growth Initiation Factors in Nature: A Putative Mechanism for in situ Cultivation of Previously Uncultivated Microorganisms

Most microorganisms resist cultivation under standard laboratory conditions. On the other hand, cultivating microbes in a membrane-bound device incubated in nature (in situ cultivation) can be an effective approach to overcome this limitation. In the present study, we applied in situ cultivation to isolate diverse previously uncultivated marine sponge-associated microbes and comparatively analyzed this method's efficiencies with those of the conventional method. Then, we attempted to investigate the key and previously unidentified mechanism of growing uncultivated microorganisms by in situ cultivation focusing on growth triggering via growth initiation factor. Significantly more novel and diverse microbial types were isolated via in situ cultivation than by standard direct plating (SDP). We hypothesized that some of environmental microorganisms which resist cultivation are in a non-growing state and require growth initiation factors for the recovery and that these can be provided from the environment (in this study from marine sponge). According to the hypothesis, the effect of the sponge extract on recovery on agar medium was compared between strains derived from in situ and SDP cultivation. Adding small amounts of the sponge extracts to the medium elevated the colony-formation efficiencies of the in situ strains at the starvation recovery step, while it showed no positive effect on that of SDP strains. Conversely, specific growth rates or saturated cell densities of all tested strains were not positively affected. These results indicate that, (1) the sponge extract contains chemical compounds that facilitate recovery of non-growing microbes, (2) these substances worked on the in situ strains, and (3) growth initiation factor in the sponge extract did not continuously promote growth activity but worked as triggers for regrowth (resuscitation from non-growing state).

A library preparation optimized for metagenomics of RNA viruses

Our understanding of the viral communities associated to animals has not yet reached the level attained on the bacteriome. This situation is due to, among others, technical challenges in adapting metagenomics using high-throughput sequencing to the study of RNA viromes in animals. Although important developments have been achieved in most steps of viral metagenomics, there is yet a key step that has received little attention: the library preparation. This situation differs from bacteriome studies in which developments in library preparation have largely contributed to the democratisation of metagenomics. Here, we present a library preparation optimized for metagenomics of RNA viruses from insect vectors of viral diseases. The library design allows a simple PCR-based preparation, such as those routinely used in bacterial metabarcoding, that is adapted to shotgun sequencing as required in viral metagenomics. We first optimized our library preparation using mock viral communities and then validated a full metagenomic approach incorporating our preparation in two pilot studies with field-caught insect vectors; one including a comparison with a published metagenomic protocol. Our approach provided a fold increase in virus-like sequences compared to other studies, and nearly-full genomes from new virus species. Moreover, our results suggested conserved trends in virome composition within a population of a mosquito species. Finally, the sensitivity of our approach was compared to a commercial diagnostic PCR for the detection of an arbovirus in field-caught insect vectors. Our approach could facilitate studies on viral communities from animals and the democratization of metagenomics in community ecology of viruses.

Detection of a pederin-like compound using a dilution-to-extinction-based platform for the isolation of marine bacteria in drug discovery strategies

The continued development of culturing technologies for the discovery of new molecules from marine microbes is of paramount importance for drug discovery. Coupled with this, the use of the high-throughput approach shows promise for increasing the number of Gram-negative and non-filamentous bacteria cultures that can be surveyed, since they show a lower potential of bioactivity. In this work, we propose a new strategy of high-throughput cultivation of bacteria inspired by a dilution-to-extinction (DTE) methodology for the isolation of, and screening for, new cytotoxic compound producing marine bacteria. A marine sponge tissue was directly used as inoculum and the results were compared with the data obtained through the direct plating isolation method. Enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC-PCR) genomic fingerprinting indicated the isolation of four bioactive strains, three of them producers of a pederin-like compound, and the fourth one able to synthesize a different compound, still unidentified, rendered by the DTE approach, in comparison with one bioactive strain identified through the plating method. Analyses based on the 16S rRNA gene data showed the existence of two different species belonging to the genus Labrenzia. The efficiency and diversity ratio in the number of isolates and compounds are discussed. In view of the results, the proposed DTE approach proved to be efficient for the isolation of new cytotoxic compounds of marine origin and pave the way for future potential applications.

Opportunities for the application of real-time bacterial cell analysis using flow cytometry for the advancement of sterilization microbiology

Medical devices provide critical care and diagnostic applications through patient contact. Sterility assurance level (SAL) may be defined as the probability of a single viable micro-organism occurring on an item after a sterilization process. Sterilization microbiology often relies upon using an overkill validation method where a 12-log reduction in recalcitrant bacterial endospore population occurs during the process that exploits conventional laboratory-based culture media for enumeration. This timely review explores key assumptions underpinning use of conventional culture-based methods in sterilization microbiology. Consideration is given to how such methods may limit the ability to fully appreciate the inactivation kinetics of a sterilization process such as vaporized hydrogen peroxide (VH2O2) sterilization, and consequently design efficient sterilization processes. Specific use of the real-time flow cytometry (FCM) is described by way of elucidating the practical relevance of these limitation factors with implications and opportunities for the sterilization industry discussed. Application of FCM to address these culture-based limitation factors will inform real-time kinetic inactivation modelling and unlock potential to embrace emerging opportunities for pharma, medical device and sterilization industries including potentially disruptive applications that may involve reduced usage of sterilant.

Characterization of Bacterial and Fungal Assemblages From Historically Contaminated Metalliferous Soils Using Metagenomics Coupled With Diffusion Chambers and Microbial Traps

The majority of environmental microbiomes are not amenable to cultivation under standard laboratory growth conditions and hence remain uncharacterized. For environmental applications, such as bioremediation, it is necessary to isolate microbes performing the desired function, which may not necessarily be the fast growing or the copiotroph microbiota. Toward this end, cultivation and isolation of microbial strains using diffusion chambers (DC) and/or microbial traps (MT) have both been recently demonstrated to be effective strategies because microbial enrichment is facilitated by soil nutrients and not by synthetically defined media, thus simulating their native habitat. In this study, DC/MT chambers were established using soils collected from two US Department of Energy (DOE) sites with long-term history of heavy metal contamination, including mercury (Hg). To characterize the contamination levels and nutrient status, soils were first analyzed for total mercury (THg), methylmercury (MeHg), total carbon (TC), total nitrogen (TN), and total phosphorus (TP). Multivariate statistical analysis on these measurements facilitated binning of soils under high, medium and low levels of contamination. Bacterial and fungal microbiomes that developed within the DC and MT chambers were evaluated using comparative metagenomics, revealing Chthoniobacter, Burkholderia and Bradyrhizobium spp., as the predominant bacteria while Penicillium, Thielavia, and Trichoderma predominated among fungi. Many of these core microbiomes were also retrieved as axenic isolates. Furthermore, canonical correspondence analysis (CCA) of biogeochemical measurements, metal concentrations and bacterial communities revealed a positive correlation of Chthoniobacter/Bradyrhizobium spp., to THg whereas Burkholderia spp., correlated with MeHg. Penicillium spp., correlated with THg whereas Trichoderma spp., and Aspergillus spp., correlated with MeHg, from the MT approach. This is the first metagenomics-based assessment, isolation and characterization of soil-borne bacterial and fungal communities colonizing the diffusion chambers (DC) and microbial traps (MT) established with long-term metal contaminated soils. Overall, this study provides proof-of-concept for the successful application of DC/MT based assessment of mercury resistant (HgR) microbiomes in legacy metal-contaminated soils, having complex contamination issues. Overall, this study brings out the significance of microbial communities and their relevance in context to heavy metal cycling for better stewardship and restoration of such historically contaminated systems.

Wolbachia megadiversity: 99% of these microorganismic manipulators unknown

Wolbachia (Alphaproteobacteria) are the most widespread endosymbionts of arthropods, manipulating their hosts by various means to maximize the number of host individuals infected. Based on quantitative analyzes of the published literature from Web of Science® and of DNA sequences of arthropod-hosted Wolbachia from GenBank, we made plausible that less than 1% of the expected 100 000 strains of Wolbachia in arthropods is known. Our findings suggest that more and globally better coordinated efforts in screening arthropods are needed to explore the true Wolbachia diversity and to help us understand the ecology and evolution of these host-endosymbiont interactions.

A progesterone biosensor derived from microbial screening

Bacteria are an enormous and largely untapped reservoir of biosensing proteins. We describe an approach to identify and isolate bacterial allosteric transcription factors (aTFs) that recognize a target analyte and to develop these TFs into biosensor devices. Our approach utilizes a combination of genomic screens and functional assays to identify and isolate biosensing TFs, and a quantum-dot Förster Resonance Energy Transfer (FRET) strategy for transducing analyte recognition into real-time quantitative measurements. We use this approach to identify a progesterone-sensing bacterial aTF and to develop this TF into an optical sensor for progesterone. The sensor detects progesterone in artificial urine with sufficient sensitivity and specificity for clinical use, while being compatible with an inexpensive and portable electronic reader for point-of-care applications. Our results provide proof-of-concept for a paradigm of microbially-derived biosensors adaptable to inexpensive, real-time sensor devices.

Mapping Microbial Capacities for Bioremediation: Genes to Genomics

Bioremediation is a process wherein the decontamination strategies are designed so that a site could achieve the environmental abiotic and biotic parameters close to its baseline. In the process, the driving force is the available microbial genetic degradative capabilities, which are supported by required nutrients so that the desired expression of these capabilities could be exploited in favour of removal of pollutants. With genomics tools not only the available abilities could be estimated but their dynamic performance could also be established. These tools are now playing important role in bioprocess optimization, which not only derive the bio-stimulation plans but also could suggest possible genetic bio-augmentation options.

Chemical Composition and Biological Activities of Metabolites from the Marine Fungi Penicillium sp. Isolated from Sediments of Co To Island, Vietnam

Marine microorganisms are an invaluable source of novel active secondary metabolites possessing various biological activities. In this study, the extraction and isolation of the marine sediment Penicillium species collected in Vietnam yielded ten secondary metabolites, including sporogen AO-1 (1), 3-indolecarbaldehyde (2), 2-[(5-methyl-1,4-dioxan-2-yl)methoxy]ethanol (3), 2-[(2R-hydroxypropanoyl)amino]benzamide (4), 4-hydroxybenzandehyde (5), chrysogine (6), 3-acetyl-4-hydroxycinnoline (7), acid 1H-indole-3-acetic (8), cyclo (Tyr-Trp) (9), and 2',3'-dihydrosorbicillin (10). Their structures were identified by the analysis of 1D and 2D NMR data. Among the isolated compounds, 2-[(5-methyl-1,4-dioxan-2-yl)methoxy]ethanol (3) showed a strong inhibitory effect against Enterococcus faecalis with a minimum inhibitory concentration value of 32 µg/mL. Both 2-[(2R-hydroxypropanoyl)amino]benzamide (4) and 4-hydroxybenzandehyde (5) selectively inhibited E. coli with minimum inhibitory concentration values of 16 and 8 µg/mL, respectively. 2',3'-Dihydrosorbicillin (10) potentially inhibited α-glucosidase activity at a concentration of 2.0 mM (66.31%).

Draft Genome Sequence of Janthinobacterium sp. Strain PC23-8, Isolated from a Freshwater Stream Impacted by Acid Mine Drainage

We present the draft genome sequence of Janthinobacterium sp. strain PC23-8, a bacterium isolated from freshwater stream sediment downstream from acid mine drainage. The 6.4-Mb genome sequence of this strain contains several secondary metabolite gene clusters, including one similar to the cyclic peptide jagaricin, synthesized by Janthinobacterium agaricidamnosum.

Metagenomic Evaluation of Bacterial and Fungal Assemblages Enriched within Diffusion Chambers and Microbial Traps Containing Uraniferous Soils

Despite significant technological advancements in the field of microbial ecology, cultivation and subsequent isolation of the vast majority of environmental microorganisms continues to pose challenges. Isolation of the environmental microbiomes is prerequisite to better understand a myriad of ecosystem services they provide, such as bioremediation of contaminants. Towards this end, in this culturomics study, we evaluated the colonization of soil bacterial and fungal communities within diffusion chambers (DC) and microbial traps (MT) established using uraniferous soils collected from a historically contaminated soil from Aiken, USA. Microbial assemblages were compared between the DC and MT relative to the native soils using amplicon based metagenomic and bioinformatic analysis. The overall rationale of this study is that DC and MT growth chambers provide the optimum conditions under which desired microbiota, identified in a previous study to serve as the “core” microbiomes, will proliferate, leading to their successful isolation. Specifically, the core microbiomes consisted of assemblages of bacteria (Burkholderia spp.) and fungi (Penicillium spp.), respectively. The findings from this study further supported previous data such that the abundance and diversity of the desired “core” microbiomes significantly increased as a function of enrichments over three consecutive generations of DC and MT, respectively. Metagenomic analysis of the DC/MT generations also revealed that enrichment and stable populations of the desired “core” bacterial and fungal microbiomes develop within the first 20 days of incubation and the practice of subsequent transfers for second and third generations, as is standard in previous studies, may be unnecessary. As a cost and time cutting measure, this study recommends running the DC/MT chambers for only a 20-day time period, as opposed to previous studies, which were run for months. In summation, it was concluded that, using the diffusion chamber-based enrichment techniques, growth of desired microbiota possessing environmentally relevant functions can be achieved in a much shorter time frame than has been previously shown.

Diluted conventional media improve the microbial cultivability from aquarium seawater

The cultivation of microbial species remains a primary challenge in microbiology and obtaining pure cultures is essential for the study of microbial physiology and function. When isolating microorganisms from aquaculture environments, Vibrio are the most dominate isolates on the media that are commonly used. In order to expand our ability to study microbial species, an easy-operation and low-cost medium that can reduce the interference of Vibrio strains and increase the cultivability of other bacteria is urgently needed. We compared viable cell counts on conventional media (CM; including Marine Agar 2216 and LB media) and diluted media (DM; including 1/10-Marine Agar 2216, 1/10-LB). We also assessed the diversity of cultivable microorganisms under high and low nutrient conditions by a plate-wash strategy coupled with high-throughput sequencing of the V4 hypervariable region of the 16S rRNA gene. The results show that microbial communities from DM, especially 1/10-Marine Agar 2216, are more diverse than those obtained from CM. Vibrio isolates were reduced on DM. PICRUSt analysis revealed that nutrient composition is a significant contributor to the diversity and function of the cultivable microbial communities. Bacteria grown on CM possess more pathogenic characteristics, whereas DM favors the growth of bacteria that have multiple metabolic functions. Collectively, our data provide strong evidence that dilution of CM influences the cultivability of bacteria from aquaculture seawater. It also supports that DM can expand the range of microbial species that can be cultivated. This study also provides insights for media design in microbial cultivation from aquaculture systems.

Metagenomics-Guided Survey, Isolation, and Characterization of Uranium Resistant Microbiota from the Savannah River Site, USA

Despite the recent advancements in culturomics, isolation of the majority of environmental microbiota performing critical ecosystem services, such as bioremediation of contaminants, remains elusive. Towards this end, we conducted a metagenomics-guided comparative assessment of soil microbial diversity and functions present in uraniferous soils relative to those that grew in diffusion chambers (DC) or microbial traps (MT), followed by isolation of uranium (U) resistant microbiota. Shotgun metagenomic analysis performed on the soils used to establish the DC/MT chambers revealed Proteobacterial phyla and Burkholderia genus to be the most abundant among bacteria. The chamber-associated growth conditions further increased their abundances relative to the soils. Ascomycota was the most abundant fungal phylum in the chambers relative to the soils, with Penicillium as the most dominant genus. Metagenomics-based taxonomic findings completely mirrored the taxonomic composition of the retrieved isolates such that the U-resistant bacteria and fungi mainly belonged to Burkholderia and Penicillium species, thus confirming that the chambers facilitated proliferation and subsequent isolation of specific microbiota with environmentally relevant functions. Furthermore, shotgun metagenomic analysis also revealed that the gene classes for carbohydrate metabolism, virulence, and respiration predominated with functions related to stress response, membrane transport, and metabolism of aromatic compounds were also identified, albeit at lower levels. Of major note was the successful isolation of a potentially novel Penicillium species using the MT approach, as evidenced by whole genome sequence analysis and comparative genomic analysis, thus enhancing our overall understanding on the uranium cycling microbiota within the tested uraniferous soils.

Distribution of Pseudomonas fluorescens and Aeromonas hydrophila Bacteria in a Recirculating Aquaculture System during Farming of European Grayling (Thymallus thymallus L.) Broodstock

Pseudomonas fluorescens and Aeromonas hydrophila bacteria are opportunistic pathogens that occur naturally in the aquatic environment and in the gut flora of healthy fish. Both species can pose a serious threat for fish that are highly sensitive to water pollution. The aim of this study was to determine the extent to which the amount of administered fish feed and fish biomass affect the distribution and abundance of Ps. fluorescens and A. hydrophila bacteria in a recirculating aquaculture system (RAS) during farming of European grayling (Thymallus thymallus L.) broodstock. A total of 68 water samples from the inflow, two rearing tanks and the outflow as well as 17 feed samples were collected and analyzed separately. Bacterial populations were analyzed by the culture-dependent method and a molecular method (fluorescence in situ hybridization, FISH) to detect culturable strains and viable but non-culturable strains, respectively. Fish biomass, feed and 16 water quality parameters (temperature, pH, concentration of dissolved oxygen, oxygen saturation, five-day biochemical oxygen demand (BOD5), total phosphorus, total organic phosphorus and nitrogen, orthophosphates, total nitrogen, nitrite and nitrate nitrogen, ammonia nitrogen, ammonium nitrogen, total suspended solids, and total organic carbon) were the explanatory factors. Statistically significant differences (RM-ANOVA, p ≤ 0.05) were stated in bacterial abundance in samples from the inflow, rearing tanks and the outflow. Water samples from the RAS were abundantly colonized by non-culturable Ps. fluorescens and A. hydrophila bacteria. Feed was not a source of bacteria, but a redundancy analysis (RDA) revealed that the amount of feed, fish biomass, BOD5, and total suspended solids and total organic carbon were positively correlated in both Ps. fluorescens and A. hydrophila. These parameters also influenced the distribution of both potentially pathogenic bacterial populations and contributed to the bacterial contamination of water in the RAS. Our results are particularly valuable for aquacultures that help to replenish wild stocks and rebuild populations of threatened species in natural aquatic environments.

Culturomics-Based Taxonomic Diversity of Bacterial Communities in the Hot Springs of Saudi Arabia

Hot springs are natural habitats for thermophilic microorganisms and provide a significant opportunity for bioprospecting thermostable biomolecules. However, the scientific community has only a fragmented understanding of the microbial diversity and composition in these biotopes. In this study, bacterial diversity in sediment samples from six hot springs of Saudi Arabia was investigated using an improved culture-dependent approach. High-throughput MALDI-TOF MS (matrix assisted laser desorption/ionization mass spectrometry) and 16S rRNA genes sequencing were used for the identification of purified isolates. Most of the hot springs had a neutral pH and a temperature range of 45-89°C. Relatively higher colony-forming units (1.9 ± 0.45 × 10⁴) were observed with 60°C incubation of an 89°C sediment sample from the hot spring at Ain al Harra1. Among the 536 purified isolates, 6 novel candidate species were found, and the remaining isolates represented 139 distinct species. Several species, such as Bacillus cereus, Bacillus subtilis, and Bacillus schlegelii, were ubiquitous in the hot springs sampled, but 102 of the identified species were uniquely distributed among the hot springs. Sixteen of the isolated thermophilic bacteria, including Geobacillus kaustophilus, Thermus oshimai, and Brevibacillus thermoruber, grew at ≥60°C. In addition, 21 species exhibited hydrolytic enzymatic activity. Most of these species belonged to Bacillus and Brevibacillus. Overall, this study contributes to global knowledgebase on bacterial communities by comprehensively profiling culture-based bacterial diversity in the hot springs of Saudi Arabia. Further studies are required for investigating bacteria from hot springs by a metagenomic approach.

Rapid Detection and Monitoring of Flavobacterium psychrophilum in Water by Using a Handheld, Field-Portable Quantitative PCR System

Advances in technology are making it easier for rapid field detection of microbes in aquaculture. Specifically, real-time quantitative PCR (qPCR) analysis, which has traditionally been confined to laboratory-based protocols, is now available in a handheld, field-portable system. The feasibility of using the Biomeme handheld qPCR system for rapid (<50 min) on-site detection and monitoring of Flavobacterium psychrophilum from filtered water samples was evaluated. Paired water samples were collected over a 23-d period from microcosm tanks that housed fish injected with known levels of F. psychrophilum. Water samples were filtered through 0.45-μm nitrocellulose filters and were analyzed with both the Biomeme qPCR platform and a traditional bench qPCR protocol. The two methods identified similar fluctuations in F. psychrophilum DNA throughout the study. Standard curves relating quantification cycles to the number of F. psychrophilum colony-forming units (CFU) were constructed and analyzed; results indicated that CFU increased rapidly between days 6 and 8 of the trial and then progressively decreased during the remaining 15 d. Average calculated log₁₀ (CFU/mL) values were significantly correlated between the two platforms. Rapid, field-based qPCR can be incorporated into daily water quality monitoring protocols to help detect and monitor microbes in aquaculture systems.

Patterns of Bird-Bacteria Associations

Birds, with their broad geographic ranges and close association with humans, have historically played an important role as carriers of human disease and as reservoirs for drug-resistant bacteria. Here, we examine scientific literature over a 15-year timespan to identify reported avian-bacterial associations and factors that may impact zoonotic disease emergence by classifying traits of bird species and their bacteria. We find that the majority of wild birds studied were migratory, in temperate habitats, and in the order Passeriformes. The highest diversity of bacteria was found on birds in natural habitats. The most frequently reported bacteria were Escherichia coli, Salmonella enterica, and Campylobacter jejuni. Of the bacteria species reported, 54% have shown pathogenicity toward humans. Percentage-wise, more pathogens were found in tropical (vs. temperate) habitats and natural (vs. suburban, urban, or agricultural) habitats. Yet, only 22% were tested for antibiotic resistance, and of those tested, 75% of bacteria species were resistant to at least one antibiotic. There were no significant patterns of antibiotic resistance in migratory versus non-migratory birds, temperate versus tropical areas, or different habitats. We discuss biases in detection and representation, and suggest a need for increased sampling in non-temperate zones and in a wider range of avian species.

Bacterial diversity of bat guano from Cabalyorisa Cave, Mabini, Pangasinan, Philippines: A first report on the metagenome of Philippine bat guano

Bats are highly diverse and ecologically valuable mammals. They serve as host to bacteria, viruses and fungi that are either beneficial or harmful to its colony as well as to other groups of cave organisms. The bacterial diversity of two bat guano samples, C1 and C2, from Cabalyorisa Cave, Mabini, Pangasinan, Philippines were investigated using 16S rRNA gene amplicon sequencing. V3-V4 hypervariable regions were amplified and then sequenced using Illumina MiSeq 250 PE system. Reads were processed using Mothur and QIIME pipelines and assigned 12,345 OTUs for C1 and 5,408 OTUs for C2. The most dominant OTUs in C1 belong to the Proteobacteria (61.7%), Actinobacteria (19.4%), Bacteroidetes (4.2%), Firmicutes (2.7%), Chloroflexi (2.5%), candidate phylum TM7 (2.3%) and Planctomycetes (1.9%) while Proteobacteria (61.7%) and Actinobacteria (34.9%) dominated C2. Large proportion of sequence reads mainly associated with unclassified bacteria indicated possible occurrence of novel bacteria in both samples. XRF spectrophotometric analyses of C1 and C2 guano revealed significant differences in the composition of both major and trace elements. C1 guano recorded high levels of Si, Fe, Mg, Al, Mn, Ti and Cu while C2 samples registered high concentrations of Ca, P, S, Zn and Cr. Community structure of the samples were compared with other published community profiling studies from Finland (SRR868695), Meghalaya, Northeast India (SRR1793374) and Maharashtra State, India (CGS). Core microbiome among samples were determined for comparison. Variations were observed among previously studied guano samples and the Cabalyorisa Cave samples were attributed to either bat sources or age of the guano. This is the first study on bacterial diversity of guano in the Philippines through high-throughput sequencing.

Metagenomic discovery of a novel transaminase for valorization of monoaromatic compounds

The profitability of next-generation biorefineries is acutely contingent on the discovery and utilization of biocatalysts that can valorize lignin. To this end, the metabolic catalogues of diverse microbiota have been mined previously using functional metagenomics in order to identify biocatalysts that can selectively degrade lignin into monoaromatic compounds. Herein, we have further improved the valorization factor of biorefining by deploying functional metagenomics toward the identification of a novel transaminase that can selectively functionalize lignin-derived monoaromatics to produce value-added feedstocks for pharmaceutical synthesis. We implemented a high-throughput colorimetric assay using o-xylylenediamine as the amino donor and successfully identified a transaminase that utilizes the canonical cofactor, pyridoxal 5'-phosphate, to aminate as many as 14 monoaromatic aldehydes and ketones. We subsequently identified the optimal conditions for enzyme activity towards the most favoured amino acceptor, benzaldehyde, including temperature, pH and choice of co-solvent. We also evaluated the specificity of the enzyme towards a variety of amino donors, as well as the optimal concentration of the most favoured amino donor. Significantly, the novel enzyme is markedly smaller than typical transaminases, and it is stably expressed in E. coli without any modifications to its amino acid sequence. Finally, we developed and implemented a computational methodology to assess the activity of the novel transaminase. The methodology is generalizable for assessing any transaminase and facilitates in silico screening of enzyme-substrate combinations in order to develop efficient biocatalytic routes to value-added amines. The computational pipeline is an ideal complement to metagenomics and opens new possibilities for biocatalyst discovery.

Harnessing microfluidic streak plate technique to investigate the gut microbiome of Reticulitermes chinensis

The termite gut microbiome is a model system to investigate microbial interactions and their associations with host. For decades, extensive research with molecular tools and conventional cultivation method has been carried out to define the microbial diversity in termite gut. Yet, many bacterial groups of the termite gut microbiome have not been successfully cultivated in laboratory. In this study, we adapted the recently developed microfluidic streak plate (MSP) technique for cultivation of termite gut microbial communities at both aerobic and anaerobic conditions. We found that 99 operational taxonomic units (OTUs) were cultivable by MSP approach and 18 OTUs were documented first time for termite gut microbiota. Further analysis of the bacterial diversities derived by culture‐dependent MSP approach and culture‐independent 16S rRNA gene typing revealed that both methods have bias in recovery of gut microbiota. In total 396 strains were isolated with MSP technique, and potential new taxa at species and/or genus levels were obtained that were phylogenetically related to Burkholderia, Micrococcus, and Dysgonomonas. Results from this study indicate that MSP technique is applicable for cultivating previously unknown and new microbial groups of termite gut microbiota.

Onge RP, Tang Y, Hillenmeyer ME. HEx: A heterologous expression platform for the discovery of fungal natural products

For decades, fungi have been a source of U.S. Food and Drug Administration-approved natural products such as penicillin, cyclosporine, and the statins. Recent breakthroughs in DNA sequencing suggest that millions of fungal species exist on Earth, with each genome encoding pathways capable of generating as many as dozens of natural products. However, the majority of encoded molecules are difficult or impossible to access because the organisms are uncultivable or the genes are transcriptionally silent. To overcome this bottleneck in natural product discovery, we developed the HEx (Heterologous EXpression) synthetic biology platform for rapid, scalable expression of fungal biosynthetic genes and their encoded metabolites in Saccharomyces cerevisiae. We applied this platform to 41 fungal biosynthetic gene clusters from diverse fungal species from around the world, 22 of which produced detectable compounds. These included novel compounds with unexpected biosynthetic origins, particularly from poorly studied species. This result establishes the HEx platform for rapid discovery of natural products from any fungal species, even those that are uncultivable, and opens the door to discovery of the next generation of natural products.

Rapid evolution of a bacterial iron acquisition system

Under iron limitation, bacteria scavenge ferric (Fe³⁺ ) iron bound to siderophores or other chelates from the environment to fulfill their nutritional requirement. In gram-negative bacteria, the siderophore uptake system prototype consists of an outer membrane transporter, a periplasmic binding protein and a cytoplasmic membrane transporter, each specific for a single ferric siderophore or siderophore family. Here, we show that spontaneous single gain-of-function missense mutations in outer membrane transporter genes of Bradyrhizobium japonicum were sufficient to confer on cells the ability to use synthetic or natural iron siderophores, suggesting that selectivity is limited primarily to the outer membrane and can be readily modified. Moreover, growth on natural or synthetic chelators required the cytoplasmic membrane ferrous (Fe²⁺ ) iron transporter FeoB, suggesting that iron is both dissociated from the chelate and reduced to the ferrous form within the periplasm prior to cytoplasmic entry. The data suggest rapid adaptation to environmental iron by facile mutation of selective outer membrane transporter genes and by non-selective uptake components that do not require mutation to accommodate new iron sources.

An Improved Whole-Cell Biosensor for the Discovery of Lignin-Transforming Enzymes in Functional Metagenomic Screens

The discovery and utilization of biocatalysts that selectively valorize lignocellulose is critical to the profitability of next-generation biorefineries. Here, we report the development of a refactored, whole-cell, GFP-based biosensor for high-throughput identification of biocatalysts that transform lignin into specialty chemicals from environmental DNA of uncultivable archaea and bacteria. The biosensor comprises the transcriptional regulator and promoter of the emrRAB operon of E. coli, and the configuration of the biosensor was tuned with the aid of mathematical model. The biosensor sensitively and selectively detects vanillin and syringaldehyde, and responds linearly over a wide detection range. We employed the biosensor to screen 42 520 fosmid clones comprising environmental DNA isolated from two coal beds and successfully identified 147 clones that transform hardwood kraft lignin to vanillin and syringaldehyde.

Exploring the Cultivable Ectocarpus Microbiome

Coastal areas form the major habitat of brown macroalgae, photosynthetic multicellular eukaryotes that have great ecological value and industrial potential. Macroalgal growth, development, and physiology are influenced by the microbial community they accommodate. Studying the algal microbiome should thus increase our fundamental understanding of algal biology and may help to improve culturing efforts. Currently, a freshwater strain of the brown macroalga Ectocarpus subulatus is being developed as a model organism for brown macroalgal physiology and algal microbiome studies. It can grow in high and low salinities depending on which microbes it hosts. However, the molecular mechanisms involved in this process are still unclear. Cultivation of Ectocarpus-associated bacteria is the first step toward the development of a model system for in vitro functional studies of brown macroalgal–bacterial interactions during abiotic stress. The main aim of the present study is thus to provide an extensive collection of cultivable E. subulatus-associated bacteria. To meet the variety of metabolic demands of Ectocarpus-associated bacteria, several isolation techniques were applied, i.e., direct plating and dilution-to-extinction cultivation techniques, each with chemically defined and undefined bacterial growth media. Algal tissue and algal growth media were directly used as inoculum, or they were pretreated with antibiotics, by filtration, or by digestion of algal cell walls. In total, 388 isolates were identified falling into 33 genera (46 distinct strains), of which Halomonas (Gammaproteobacteria), Bosea (Alphaproteobacteria), and Limnobacter (Betaproteobacteria) were the most abundant. Comparisons with 16S rRNA gene metabarcoding data showed that culturability in this study was remarkably high (∼50%), although several cultivable strains were not detected or only present in extremely low abundance in the libraries. These undetected bacteria could be considered as part of the rare biosphere and they may form the basis for the temporal changes in the Ectocarpus microbiome.

Bioprospecting of novel thermostable β-glucosidase from Bacillus subtilis RA10 and its application in biomass hydrolysis

BACKGROUND

Saccharification is the most crucial and cost-intensive process in second generation biofuel production. The deficiency of β-glucosidase in commercial enzyme leads to incomplete biomass hydrolysis. The decomposition of biomass at high temperature environments leads us to isolate thermotolerant microbes with β-glucosidase production potential.

RESULTS

A total of 11 isolates were obtained from compost and cow dung samples that were able to grow at 50 °C. On the basis of qualitative and quantitative estimation of β-glucosidase enzyme production, Bacillus subtilis RA10 was selected for further studies. The medium components and growth conditions were optimized and β-glucosidase enzyme production was enhanced up to 19.8-fold. The β-glucosidase from B. subtilis RA10 retained 78% of activity at 80 °C temperature and 68.32% of enzyme activity was stable even at 50 °C after 48 h of incubation. The supplementation of β-glucosidase from B. subtilis RA10 into commercial cellulase enzyme resulted in 1.34-fold higher glucose release. Furthermore, β-glucosidase was also functionally elucidated by cloning and overexpression of full length GH1 family β-glucosidase gene from B. subtilis RA10. The purified protein was characterized as thermostable β-glucosidase enzyme.

CONCLUSIONS

The thermostable β-glucosidase enzyme from B. subtilis RA10 would facilitate efficient saccharification of cellulosic biomass into fermentable sugar. Consequently, after saccharification, thermostable β-glucosidase enzyme would be recovered and reused to reduce the cost of overall bioethanol production process.

Evidence of horizontal gene transfer by transposase gene analyses in Fervidobacterium species

Horizontal Gene Transfer (HGT) plays an important role in the physiology and evolution of microorganisms above all thermophilic prokaryotes. Some members of the Phylum Thermotogae (i.e., Thermotoga spp.) have been reported to present genomes constituted by a mosaic of genes from a variety of origins. This study presents a novel approach to search on the potential plasticity of Fervidobacterium genomes using putative transposase-encoding genes as the target of analysis. Transposases are key proteins involved in genomic DNA rearrangements. A comprehensive comparative analysis, including phylogeny, non-metric multidimensional scaling analysis of tetranucleotide frequencies, repetitive flanking sequences and divergence estimates, was performed on the transposase genes detected in four Fervidobacterium genomes: F. nodosum, F. pennivorans, F. islandicum and a new isolate (Fervidobacterium sp. FC2004). Transposase sequences were classified in different groups by their degree of similarity. The different methods used in this study pointed that over half of the transposase genes represented putative HGT events with closest relative sequences within the phylum Firmicutes, being Caldicellulosiruptor the genus showing highest gene sequence proximity. These results confirmed a direct evolutionary relationship through HGT between specific Fervidobacterium species and thermophilic Firmicutes leading to potential gene sequence and functionality sharing to thrive under similar environmental conditions. Transposase-encoding genes represent suitable targets to approach the plasticity and potential mosaicism of bacterial genomes.

The Ecology of Acidophilic Microorganisms in the Corroding Concrete Sewer Environment

Concrete corrosion is one of the most significant problems affecting valuable sewer infrastructure on a global scale. This problem occurs in the aerobic zone of the sewer, where a layer of surface corrosion develops on the exposed concrete and the surface pH is typically lowered from around 11–10 (pristine concrete) to pH 2–4. Acidophilic microorganisms become established as biofilms within the concrete corrosion layer and enhance the loss of concrete mass. Until recently, the acidophilic community was considered to comprise relatively few species of microorganisms, however, the biodiversity of the corrosion community is now recognized as being extensive and varying from different sewer environmental conditions. The diversity of acidophiles in the corrosion communities includes chemolithoautotrophs, chemolithoheterotrophs, and chemoorganoheterotrophs. The activity of these microorganisms is strongly affected by H₂S levels in the sewer gas phase, although CO₂, organic matter, and iron in the corrosion layer influence this acidic ecosystem. This paper briefly presents the conditions within the sewer that lead to the development of concrete corrosion in that environment. The review focuses on the acidophilic microorganisms detected in sewer corrosion environments, and then summarizes their proposed functions and physiology, especially in relation to the corrosion process. To our knowledge, this is the first review of acidophilic corrosion microbial communities, in which, the ecology and the environmental conditions (when available) are considered. Ecological studies of sewer corrosion are limited, however, where possible, we summarize the important metabolic functions of the different acidophilic species detected in sewer concrete corrosion layers. It is evident that microbial functions in the acidic sewer corrosion environment can be linked to those occurring in the analogous acidic environments of acid mine drainage and bioleaching.