Unearthing the power of microbes as plant microbiome for sustainable agriculture

In recent years, research into the complex interactions and crosstalk between plants and their associated microbiota, collectively known as the plant microbiome has revealed the pivotal role of microbial communities for promoting plant growth and health. Plants have evolved intricate relationships with a diverse array of microorganisms inhabiting their roots, leaves, and other plant tissues. This microbiota mainly includes bacteria, archaea, fungi, protozoans, and viruses, forming a dynamic and interconnected network within and around the plant. Through mutualistic or cooperative interactions, these microbes contribute to various aspects of plant health and development. The direct mechanisms of the plant microbiome include the enhancement of plant growth and development through nutrient acquisition. Microbes have the ability to solubilize essential minerals, fix atmospheric nitrogen, and convert organic matter into accessible forms, thereby augmenting the nutrient pool available to the plant. Additionally, the microbiome helps plants to withstand biotic and abiotic stresses, such as pathogen attacks and adverse environmental conditions, by priming the plant's immune responses, antagonizing phytopathogens, and improving stress tolerance. Furthermore, the plant microbiome plays a vital role in phytohormone regulation, facilitating hormonal balance within the plant. This regulation influences various growth processes, including root development, flowering, and fruiting. Microbial communities can also produce secondary metabolites, which directly or indirectly promote plant growth, development, and health. Understanding the functional potential of the plant microbiome has led to innovative agricultural practices, such as microbiome-based biofertilizers and biopesticides, which harness the power of beneficial microorganisms to enhance crop yields while reducing the dependency on chemical inputs. In the present review, we discuss and highlight research gaps regarding the plant microbiome and how the plant microbiome can be used as a source of single and synthetic bioinoculants for plant growth and health.

Metagenomics uncovers microbiome and resistome in soil and reindeer faeces from Ny-Ålesund (Svalbard, High Arctic)

Research on the microbiome and resistome in polar environments, such as the Arctic, is crucial for understanding the emergence and spread of antibiotic resistance genes (ARGs) in the environment. In this study, soil and reindeer faeces samples collected from Ny-Ålesund (Svalbard, High Arctic) were examined to analyze the microbiome, ARGs, and biocide/metal resistance genes (BMRGs). The dominant phyla in both soil and faeces were Pseudomonadota, Actinomycetota, and Bacteroidota. A total of 2618 predicted Open Reading Frames (ORFs) containing antibiotic resistance genes (ARGs) were detected. These ARGs belong to 162 different genes across 17 antibiotic classes, with rifamycin and multidrug resistance genes being the most prevalent. We focused on investigating antibiotic resistance mechanisms in the Ny-Ålesund environment by analyzing the resistance genes and their biological pathways. Procrustes analysis demonstrated a significant correlation between bacterial communities and ARG/BMRG profiles in soil and faeces samples. Correlation analysis revealed that Pseudomonadota contributed most to multidrug and triclosan resistance, while Actinomycetota were predominant contributors to rifamycin and aminoglycoside resistance. The geochemical factors, SiO42- and NH4+, were found to significantly influence the microbial composition and ARG distribution in the soil samples. Analysis of ARGs, BMRGs, virulence factors (VFs), and pathogens identified potential health risks associated with certain bacteria, such as Cryobacterium and Pseudomonas, due to the presence of different genetic elements. This study provided valuable insights into the molecular mechanisms and geochemical factors contributing to antibiotic resistance and enhanced our understanding of the evolution of antibiotic resistance genes in the environment.

Cultivation of Diverse Novel Marine Bacteria from Deep Ocean Sediment Using Spent Culture Supernatant of Ca. Bathyarchaeia Enrichment

Most microorganisms resist pure cultivation under conventional laboratory conditions. One of the primary issues for this un-culturability is the absence of biologically produced growth-promoting factors in traditionally defined growth media. However, whether cultivating microbes by providing spent culture supernatant of pivotal microbes in the growth medium can be an effective approach to overcome this limitation is still an under-explored area of research. Here, we used the spent culture medium (SCM) method to isolate previously uncultivated marine bacteria and compared the efficiency of this method with the traditional cultivation (TC) method. In the SCM method, Ca. Bathyarchaeia-enriched supernatant (10%) was used along with recalcitrant organic substrates such as lignin, humic acid, and organic carbon mixture. Ca. Bathyarchaeia, a ubiquitous class of archaea, have the capacity to produce metabolites, making their spent culture supernatant a key source to recover new bacterial stains. Both cultivation methods resulted in the recovery of bacterial species from the phyla Pseudomonadota, Bacteroidota, Actinomycetota, and Bacillota. However, our SCM approach also led to the recovery of species from rarely cultivated groups, such as Planctomycetota, Deinococcota, and Balneolota. In terms of the isolation of new taxa, the SCM method resulted in the cultivation of 80 potential new strains, including one at the family, 16 at the genus, and 63 at the species level, with a novelty ratio of ~ 35% (80/219). In contrast, the TC method allowed the isolation of ~ 10% (19/171) novel strains at species level only. These findings suggest that the SCM approach improved the cultivation of novel and diverse bacteria.

Autoclaving is at least as effective as gamma irradiation for biotic clearing and intentional microbial recolonization of soil

Sterilization is commonly used to remove or reduce the biotic constraints of a soil to allow recolonization by soil-dwelling organisms, with autoclaving and gamma irradiation being the most frequently used approaches. Many studies have characterized sterilization impacts on soil physicochemical properties, with gamma irradiation often described as the preferred approach, despite the lower cost and higher scalability of autoclaving. However, few studies have compared how sterilization techniques impact soil recolonization by microorganisms. Here, we compared how two sterilization approaches (autoclaving; gamma irradiation) and soil washing impacted microbial recolonization of soil from a diverse soil inoculum. Sterilization method had little impact on microbial alpha diversity across recolonized soils. For sterile soil regrowth microcosms, species richness and diversity were significantly reduced by autoclaving relative to gamma irradiation, particularly for fungi. There was no impact of sterilization method on bacterial composition in recolonized soils and minimal impact on fungal composition (P = 0.05). Washing soils had a greater impact on microbial composition than sterilization method, and sterile soil regrowth had negligible impacts on microbial recolonization. These data suggest that sterilization method has no clear impact on microbial recolonization, at least across the soils tested, indicating that soil autoclaving is an appropriate and economical approach for biotically clearing soils.IMPORTANCESterilized soils represent soil-like environments that act as a medium to study microbial colonization dynamics in more "natural" settings relative to artificial culturing environments. Soil sterilization is often carried out by gamma irradiation or autoclaving, which both alter soil properties, but gamma irradiation is thought to be the gentler technique. Gamma irradiation can be cost prohibitive and does not scale well for larger experiments. We sought to examine how soil sterilization technique can impact microbial colonization, and additionally looked at the impact of soil washing which is believed to remove soil toxins that inhibit soil recolonization. We found that both gamma-irradiated and autoclaved soils showed similar colonization patterns when reintroducing microorganisms. Soil washing, relative to sterilization technique, had a greater impact on which microorganisms were able to recolonize the soil. When allowing sterilized soils to regrow (i.e., persisting microorganisms), gamma irradiation performed worse, suggesting that gamma irradiation does not biotically clear soils as well as autoclaving. These data suggest that both sterilization techniques are comparable, and that autoclaving may be more effective at biotically clearing soil.

An untargeted cultivation approach revealed Pseudogemmatithrix spongiicola gen. nov., sp. nov., and sheds light on the gemmatimonadotal mode of cell division: binary fission

Members of the phylum Gemmatimonadota can account for up to 10% of the phylogenetic diversity in bacterial communities. However, a detailed investigation of their cell biology and ecological roles is restricted by currently only six characterized species. By combining low-nutrient media, empirically determined inoculation volumes and long incubation times in a 96-well plate cultivation platform, we isolated two strains from a limnic sponge that belong to this under-studied phylum. The characterization suggests that the two closely related strains constitute a novel species of a novel genus, for which we introduce the name Pseudogemmatithrix spongiicola. The here demonstrated isolation of novel members from an under-studied bacterial phylum substantiates that the cultivation platform can provide access to axenic bacterial cultures from various environmental samples. Similar to previously described members of the phylum, the novel isolates form spherical appendages at the cell poles that were believed to be daughter cells resulting from asymmetric cell division by budding. However, time-lapse microscopy experiments and quantitative image analysis showed that the spherical appendages never grew or divided. Although the role of these spherical cells remains enigmatic, our data suggests that cells of the phylum Gemmatimonadota divide via FtsZ-based binary fission with different division plane localization patterns than in other bacterial phyla.

Comparison of Culture-Dependent and Culture-Independent Methods for Routine Identification of Airborne Microorganisms in Speleotherapeutic Caves

The effective identification of bacterial and fungal isolates is essential for microbiological monitoring in environments like speleotherapeutic caves. This study compares MALDI-TOF MS and the OmniLog ID System, two high-throughput culture-based identification methods. MALDI-TOF MS identified 80.0% of bacterial isolates to the species level, while the OmniLog ID System identified 92.9%. However, species-level matches between the methods were only 48.8%, revealing considerable discrepancies. For discrepant results, MALDI-TOF MS matched molecular identification at the genus level in 90.5% of cases, while the OmniLog ID System matched only in 28.6%, demonstrating MALDI-TOF MS's superiority. The OmniLog ID System had difficulties identifying genera from the order Micrococcales. Fungal identification success with MALDI-TOF MS was 30.6% at the species level, potentially improvable with a customised spectral library, compared to the OmniLog ID System's 16.7%. Metagenomic approaches detected around 100 times more microbial taxa than culture-based methods, highlighting human-associated microorganisms, especially Staphylococcus spp. In addition to Staphylococcus spp. and Micrococcus spp. as indicators of cave anthropisation, metagenomics revealed another indicator, Cutibacterium acnes. This study advocates a multi-method approach combining MALDI-TOF MS, the OmniLog ID System, culture-based, and metagenomic analyses for comprehensive microbial identification. Metagenomic sampling on nitrocellulose filters provided superior read quality and microbial representation over liquid sampling, making it preferable for cave air sample collection.

A Ranking Tool for "Category Killer" Microbial Biobanks

Microbial biobanks preserve and provide microbial bioresources for research, training, and quality control purposes. They ensure the conservation of biodiversity, contribute to taxonomical research, and support scientific advancements. Microbial biobanks can cover a wide range of phylogenetic and metabolic diversity ("category killers") or focus on specific taxonomic, thematic, or disease areas. The strategic decisions about strain selection for certain applications or for the biobank culling necessitate a method to support prioritization and selection. Here, we propose an unbiased scoring approach based on objective parameters to assess, categorize, and assign priorities among samples in stock in a microbial biobank. We describe the concept of this ranking tool and its application to identify high-priority strains for whole genome sequencing with two main goals: (i) genomic characterization of quality control, reference, and type strains; (ii) genome mining for the discovery of natural products, bioactive and antimicrobial molecules, with focus on human diseases. The general concept of the tool can be useful to any biobank and for any ranking or culling needs.

Microbiome modeling: a beginner's guide

Microbiomes, comprised of diverse microbial species and viruses, play pivotal roles in human health, environmental processes, and biotechnological applications and interact with each other, their environment, and hosts via ecological interactions. Our understanding of microbiomes is still limited and hampered by their complexity. A concept improving this understanding is systems biology, which focuses on the holistic description of biological systems utilizing experimental and computational methods. An important set of such experimental methods are metaomics methods which analyze microbiomes and output lists of molecular features. These lists of data are integrated, interpreted, and compiled into computational microbiome models, to predict, optimize, and control microbiome behavior. There exists a gap in understanding between microbiologists and modelers/bioinformaticians, stemming from a lack of interdisciplinary knowledge. This knowledge gap hinders the establishment of computational models in microbiome analysis. This review aims to bridge this gap and is tailored for microbiologists, researchers new to microbiome modeling, and bioinformaticians. To achieve this goal, it provides an interdisciplinary overview of microbiome modeling, starting with fundamental knowledge of microbiomes, metaomics methods, common modeling formalisms, and how models facilitate microbiome control. It concludes with guidelines and repositories for modeling. Each section provides entry-level information, example applications, and important references, serving as a valuable resource for comprehending and navigating the complex landscape of microbiome research and modeling.

Metagenomic exploration of cold-active enzymes for detergent applications: Characterization of a novel, cold-active and alkali-stable GH8 endoglucanase from ikaite columns in SW Greenland

Microbial communities from extreme environments are largely understudied, but are essential as producers of metabolites, including enzymes, for industrial processes. As cultivation of most microorganisms remains a challenge, culture-independent approaches for enzyme discovery in the form of metagenomics to analyse the genetic potential of a community are rapidly becoming the way forward. This study focused on analysing a metagenome from the cold and alkaline ikaite columns in Greenland, identifying 282 open reading frames (ORFs) that encoded putative carbohydrate-modifying enzymes with potential applications in, for example detergents and other processes where activity at low temperature and high pH is desired. Seventeen selected ORFs, representing eight enzyme families were synthesized and expressed in two host organisms, Escherichia coli and Aliivibrio wodanis. Aliivibrio wodanis demonstrated expression of a more diverse range of enzyme classes compared to E. coli, emphasizing the importance of alternative expression systems for enzymes from extremophilic microorganisms. To demonstrate the validity of the screening strategy, we chose a recombinantly expressed cellulolytic enzyme from the metagenome for further characterization. The enzyme, Cel240, exhibited close to 40% of its relative activity at low temperatures (4°C) and demonstrated endoglucanase characteristics, with a preference for cellulose substrates. Despite low sequence similarity with known enzymes, computational analysis and structural modelling confirmed its cellulase-family affiliation. Cel240 displayed activity at low temperatures and good stability at 25°C, activity at alkaline pH and increased activity in the presence of CaCl2, making it a promising candidate for detergent and washing industry applications.

Meta-omics assisted microbial gene and strain resources mining in contaminant environment

Human activities have led to the release of various environmental pollutants, triggering ecological challenges. In situ, microbial communities in these contaminated environments are usually assumed to possess the potential capacity of pollutant degradation. However, the majority of genes and microorganisms in these environments remain uncharacterized and uncultured. The advent of meta-omics provided culture-independent solutions for exploring the functional genes and microorganisms within complex microbial communities. In this review, we highlight the applications and methodologies of meta-omics in uncovering of genes and microbes from contaminated environments. These findings may assist in future bioremediation research.

Planctoellipticum variicoloris gen. nov., sp. nov., a novel member of the family Planctomycetaceae isolated from wastewater of the aeration lagoon of a sugar processing plant in Northern Germany

In the present study, we characterise a strain isolated from the wastewater aeration lagoon of a sugar processing plant in Schleswig (Northern Germany) by Heinz Schlesner. As a pioneer in planctomycetal research, he isolated numerous strains belonging to the phylum Planctomycetota from aquatic habitats around the world. Phylogenetic analyses show that strain SH412T belongs to the family Planctomycetaceae and shares with 91.6% the highest 16S rRNA gene sequence similarity with Planctopirus limnophila DSM 3776T. Its genome has a length of 7.3 Mb and a G + C content of 63.6%. Optimal growth of strain SH412T occurs at pH 7.0-7.5 and 28 °C with its pigmentation depending on sunlight exposure. Strain SH412T reproduces by polar asymmetric division ("budding") and forms ovoid cells. The cell size determination was performed using a semi-automatic pipeline, which we first evaluated with the model species P. limnophila and then applied to strain SH412T. Furthermore, the data acquired during time-lapse analyses suggests a lifestyle switch from flagellated daughter cells to non-flagellated mother cells in the subsequent cycle. Based on our data, we suggest that strain SH412T represents a novel species within a novel genus, for which we propose the name Planctoellipticum variicoloris gen. nov., sp. nov., with strain SH412T (= CECT 30430T = STH00996T, the STH number refers to the Jena Microbial Resource Collection JMRC) as the type strain of the new species.

Cultivating the uncultured: Harnessing the "sandwich agar plate" approach to isolate heme-dependent bacteria from marine sediment

In the classical microbial isolation technique, the isolation process inevitably destroys all microbial interactions and thus makes it difficult to culture the many microorganisms that rely on these interactions for survival. In this study, we designed a simple coculture technique named the "sandwich agar plate method," which maintains microbial interactions throughout the isolation and pure culture processes. The total yield of uncultured species in sandwich agar plates based on eight helper strains was almost 10-fold that of the control group. Many uncultured species displayed commensal lifestyles. Further study found that heme was the growth-promoting factor of some marine commensal bacteria. Subsequent genomic analysis revealed that heme auxotrophies were common in various biotopes and prevalent in many uncultured microbial taxa. Moreover, our study supported that the survival strategies of heme auxotrophy in different habitats varied considerably. These findings highlight that cocultivation based on the "sandwich agar plate method" could be developed and used to isolate more uncultured bacteria.

A type III polyketide synthase cluster in the phylum Planctomycetota is involved in alkylresorcinol biosynthesis

Members of the bacterial phylum Planctomycetota have recently emerged as promising and for the most part untapped sources of novel bioactive compounds. The characterization of more than 100 novel species in the last decade stimulated recent bioprospection studies that start to unveil the chemical repertoire of the phylum. In this study, we performed systematic bioinformatic analyses based on the genomes of all 131 described members of the current phylum focusing on the identification of type III polyketide synthase (PKS) genes. Type III PKSs are versatile enzymes involved in the biosynthesis of a wide array of structurally diverse natural products with potent biological activities. We identified 96 putative type III PKS genes of which 58 are encoded in an operon with genes encoding a putative oxidoreductase and a methyltransferase. Sequence similarities on protein level and the genetic organization of the operon point towards a functional link to the structurally related hierridins recently discovered in picocyanobacteria. The heterologous expression of planctomycetal type III PKS genes from strains belonging to different families in an engineered Corynebacterium glutamicum strain led to the biosynthesis of pentadecyl- and heptadecylresorcinols. Phenotypic assays performed with the heterologous producer strains and a constructed type III PKS gene deletion mutant suggest that the natural function of the identified compounds differs from that confirmed in other bacterial alkylresorcinol producers. KEY POINTS: • Planctomycetal type III polyketide synthases synthesize long-chain alkylresorcinols. • Phylogenetic analyses suggest an ecological link to picocyanobacterial hierridins. • Engineered C. glutamicum is suitable for an expression of planctomycete-derived genes.

Leveraging genomic information to predict environmental preferences of bacteria

Genomic information is now available for a broad diversity of bacteria, including uncultivated taxa. However, we have corresponding knowledge on environmental preferences (i.e. bacterial growth responses across gradients in oxygen, pH, temperature, salinity, and other environmental conditions) for a relatively narrow swath of bacterial diversity. These limits to our understanding of bacterial ecologies constrain our ability to predict how assemblages will shift in response to global change factors, design effective probiotics, or guide cultivation efforts. We need innovative approaches that take advantage of expanding genome databases to accurately infer the environmental preferences of bacteria and validate the accuracy of these inferences. By doing so, we can broaden our quantitative understanding of the environmental preferences of the majority of bacterial taxa that remain uncharacterized. With this perspective, we highlight why it is important to infer environmental preferences from genomic information and discuss the range of potential strategies for doing so. In particular, we highlight concrete examples of how both cultivation-independent and cultivation-dependent approaches can be integrated with genomic data to develop predictive models. We also emphasize the limitations and pitfalls of these approaches and the specific knowledge gaps that need to be addressed to successfully expand our understanding of the environmental preferences of bacteria.

Integration of molecular and computational approaches paints a holistic portrait of obscure metabolisms

Microorganisms are essential drivers of earth's geochemical cycles. However, the significance of elemental redox cycling mediated by microorganisms is often underestimated beyond the most well-studied nutrient cycles. Phosphite, (per)chlorate, and iodate are each considered esoteric substrates metabolized by microorganisms. However, recent investigations have indicated that these metabolisms are widespread and ubiquitous, affirming a need to continue studying the underlying microbiology to understand their biogeochemical effects and their interface with each other and our biosphere. This review focuses on combining canonical techniques of culturing microorganisms with modern omic approaches to further our understanding of obscure metabolic pathways and elucidate their importance in global biogeochemical cycles. Using these approaches, marker genes of interest have already been identified for phosphite, (per)chlorate, and iodate using traditional microbial physiology and genetics. Subsequently, their presence was queried to reveal the distribution of metabolic pathways in the environment using publicly available databases. In conjunction with each other, computational and experimental techniques provide a more comprehensive understanding of the location of these microorganisms, their underlying biochemistry and genetics, and how they tie into our planet's geochemical cycles.

Exploring Acetogenesis in Firmicutes: From Phylogenetic Analysis to Solid Medium Cultivation with Solid-Phase Electrochemical Isolation Equipments

This study introduces a groundbreaking approach for the exploration and utilization of electrotrophic acetogens, essential for advancing microbial electrosynthesis systems (MES). Our initial focus was the development of Solid-Phase Electrochemical Isolation Equipment (SPECIEs), a novel cultivation method for isolating electrotrophic acetogens directly from environmental samples on a solid medium. SPECIEs uses electrotrophy as a selection pressure, successfully overcoming the traditional cultivation method limitations and enabling the cultivation of diverse microbial communities with enhanced specificity towards acetogens. Following the establishment of SPECIEs, we conducted a genome-based phylogenetic analysis using the Genome Taxonomy Database (GTDB) to identify potential electrotrophic acetogens within the Firmicutes phylum and its related lineages. Subsequently, we validated the electrotrophic capabilities of selected strains under electrode-oxidizing conditions in a liquid medium. This sequential approach, integrating innovative cultivation techniques with detailed phylogenetic analysis, paves the way for further advances in microbial cultivation and the identification of new biocatalysts for sustainable energy applications.

Enhancing the Conventional Culture: the Evaluation of Several Culture Media and Growth Conditions Improves the Isolation of Ruminal Bacteria

The rumen microbiota is critical in cattle digestion. Still, its low cultivability makes it difficult to study its ecological function and biotechnological potential. To improve the recovery of ruminal microorganisms, this study combined the evaluation of several cultivation parameters with metabarcoding analysis. The parameters tested comprised eight media cultures, three sample dilutions (10-2, 10-6, 10-12), and two incubation times (3 and 7 days). Bacterial populations were determined through Illumina sequencing of 16S rRNA from three biological replicates. The results indicate that none of the culture media recovered all rumen populations and that there was an altered relative abundance of the dominant phyla. In the rumen, Bacteroidetes and Firmicutes comprised 75% and 15% of the relative abundance, respectively, while in the culture media, these were 15% and 60%, respectively. Principal coordinate analysis (PCoA) of the bacterial community revealed significant shifts in population composition due to dilution, with 10-2 and 10-6 dilutions clustered closely while the 10-12 dilution differed markedly. In contrast, incubation duration did not influence population diversity. According to the results, two media, CAN and KNT, were selected based on their ability to recover more similar populations compared to the rumen sample. The metataxonomic study showed that CAN media had consistent reproducibility over time, while KNT showed enrichment of different taxa due to the use of rumen fluid as a substrate. From these, 64 pure cultures were obtained and 54 were identified through 16S rRNA gene sequencing. Being Streptococcus the most frequently isolated genus, this prevalence contrasts with the liquid media composition, underscoring the importance of refining single colony isolation strategies. Although no culture medium could replicate the native rumen bacterial population perfectly, our findings highlight the potential of CAN and KNT media in recovering populations that are more closely aligned to natural rumen conditions. In conclusion, our study emphasizes the importance of integrating molecular approaches in selecting suitable cultivation media and parameters to depict rumen bacteria accurately.

In situ Tracking of Exoenzyme Activity Using Droplet Luminescence Concentrators for Ratiometric Detection of Bacteria

We demonstrate a novel, rapid, and cost-effective biosensing paradigm that is based on an in situ visualization of bacterial exoenzyme activity using biphasic Janus emulsion droplets. Sensitization of the droplets toward dominant extracellular enzymes of bacterial pathogens is realized via selective functionalization of one hemisphere of Janus droplets with enzyme-cleavable surfactants. Surfactant cleavage results in an interfacial tension increase at the respective droplet interface, which readily transduces into a microscopically detectable change of the internal droplet morphologies. A macroscopic fluorescence read-out of such morphological transitions is obtained via ratiometrically recording the angle-dependent anisotropic emission signatures of perylene-containing droplets from two different angles. The optical read-out method facilitates detection of marginal morphological responses of polydisperse droplet samples that can be easily produced in any environment. The performance of Janus droplets as powerful optical transducers and signal amplifiers is highlighted by rapid (<4 h) and cost-effective antibody and DNA-free identification of three major foodborne pathogens, with detection thresholds of below 10 CFU mL-1 for Salmonella and <102 to 103 CFU mL-1 for Listeria and Escherichia coli.

A domesticated photoautotrophic microbial community as a biofilm model system for analyzing the influence of plastic surfaces on invertebrate grazers in limnic environments

The environmental fate of plastic particles in water bodies is influenced by microbial biofilm formation. Invertebrate grazers may be affected when foraging biofilms on plastics compared to biofilms on natural substrata but the mechanistic basis for these effects is unknown. For analyzing these effects in ecotoxicological assays stable and reproducible biofilm communities are required that are related to the environmental site of interest. Here, a defined biofilm community was established and used to perform grazing experiments with a freshwater snail. For this, snippets of different plastic materials were incubated in the photic zone of three different freshwater sites. Amplicon sequencing of biofilms formed on these snippets showed that the site of incubation and not the plastic material dominated the microbial community composition. From these biofilms, individual microbial strains as well as photoautotrophic consortia were isolated; these consortia consisted of heterotrophic bacteria that were apparently nourished by microalga. While biofilms formed by defined dual cultures of a microalga and an Alphaproteobacterium were not accepted by the snail P. fontinalis, a photoautotrophic consortium (Co_3) sustained growth and metabolism of this grazer. Amplicon sequencing revealed that consortium Co_3, which could be stably maintained on solid medium under photoautotrophic conditions, reproducibly formed biofilms of a defined composition on three different plastic materials and on glass surfaces. In conclusion, our study shows that the generation of domesticated photoautotrophic microbial communities is a valid novel approach for establishing laboratory ecotoxicological assays with higher environmental relevance than those based on defined microbiota.

Metagenomic analysis of ecological niche overlap and community collapse in microbiome dynamics

Species utilizing the same resources often fail to coexist for extended periods of time. Such competitive exclusion mechanisms potentially underly microbiome dynamics, causing breakdowns of communities composed of species with similar genetic backgrounds of resource utilization. Although genes responsible for competitive exclusion among a small number of species have been investigated in pioneering studies, it remains a major challenge to integrate genomics and ecology for understanding stable coexistence in species-rich communities. Here, we examine whether community-scale analyses of functional gene redundancy can provide a useful platform for interpreting and predicting collapse of bacterial communities. Through 110-day time-series of experimental microbiome dynamics, we analyzed the metagenome-assembled genomes of co-occurring bacterial species. We then inferred ecological niche space based on the multivariate analysis of the genome compositions. The analysis allowed us to evaluate potential shifts in the level of niche overlap between species through time. We hypothesized that community-scale pressure of competitive exclusion could be evaluated by quantifying overlap of genetically determined resource-use profiles (metabolic pathway profiles) among coexisting species. We found that the degree of community compositional changes observed in the experimental microbiome was correlated with the magnitude of gene-repertoire overlaps among bacterial species, although the causation between the two variables deserves future extensive research. The metagenome-based analysis of genetic potential for competitive exclusion will help us forecast major events in microbiome dynamics such as sudden community collapse (i.e., dysbiosis).

The effectiveness of artificial microbial community selection: a conceptual framework and a meta-analysis

The potential for artificial selection at the community level to improve ecosystem functions has received much attention in applied microbiology. However, we do not yet understand what conditions in general allow for successful artificial community selection. Here we propose six hypotheses about factors that determine the effectiveness of artificial microbial community selection, based on previous studies in this field and those on multilevel selection. In particular, we emphasize selection strategies that increase the variance among communities. We then report a meta-analysis of published artificial microbial community selection experiments. The reported responses to community selection were highly variable among experiments; and the overall effect size was not significantly different from zero. The effectiveness of artificial community selection was greater when there was no migration among communities, and when the number of replicated communities subjected to selection was larger. The meta-analysis also suggests that the success of artificial community selection may be contingent on multiple necessary conditions. We argue that artificial community selection can be a promising approach, and suggest some strategies for improving the performance of artificial community selection programs.

Genital mycoplasma infection: a systematic review and meta-analysis

BACKGROUND

Recent studies have suggested that genital mycoplasma infections may be associated with male infertility. However, this association remains controversial due to time lapse, sample size, and regional prevalence.

OBJECTIVES

This study aimed to systematically evaluate the relationship between genital mycoplasma and male infertility through a meta-analysis and to provide a basis for the clinical management of male infertility.

METHODS

We conducted a search on PubMed, EMBASE, the Cochrane Library, and CNKI databases, from January 2000 to June 2023 to identify case-control studies on the interrelationship between genital mycoplasma infection and male infertility. Two independent researchers performed an assessment of the methodological quality of trials according to the Newcastle-Ottawa scale and extracted data strictly based on the inclusion and exclusion criteria, and afterward, we carried out a meta-analysis using Stata 16.0. Pooled odds ratios (OR) with 95% confidence intervals (CI) were used to assess this relationship.

RESULTS

This meta-analysis included 21 studies from seven countries with a total of 53025 infertility cases and 6435 controls; the age range of the participating men was from 20 to 59 years old. The results obtained showed a higher prevalence of M. genitalium, M. hominis and U. urealyticum infections in infertile men than in the controls, with the opposite result for U. parvum (M. genitalium, OR, 3.438 [95% CI: 1.780, 6.643], with P = 0.000; M. hominis, OR, 1.840 [95% CI: 1.013, 3.343], with P = 0.045; U. urealyticum, OR, 3.278 [95% CI: 2.075, 5.180], with P = 0.000; U. parvum, OR, 1.671 [95% CI: 0.947, 2.950], with P = 0.077). Further, two subgroup analyses also showed that M. hominis and U. urealyticum infections were strongly associated with male infertility in China (M. hominis, P = 0.009; U. urealyticum, P = 0.000); however, M. hominis and U. urealyticum infection was not strongly associated with male infertility worldwide (M. hominis, P = 0.553; U. urealyticum, P = 0.050).

CONCLUSION

This meta-analysis revealed that male infertility was significantly associated with M. genitalium, M. hominis and U. urealyticum infections, while U. parvum infection was not. Further, our study showed that genital mycoplasma infection influences male infertility and provides a basis for future treatment.

A 3D printed plastic frame deeply impacts yeast cell growth

Solid State Fermentation (SSF) processes have been explored for yeast growth and protein and metabolites production. However, most of these processes lack standardization. In this work, we present a polylactic acid (PLA) 3D printed matrix that dramatically enhances yeast growth when embedded in liquid media compared to equivalent static cultures, and changes yeast expression patterns at the proteome level (data are available via ProteomeXchange with identifier PXD043759). Moreover, differences in sugar assimilation and ethanol production, as the main product of alcoholic fermentation, are observed. Our results suggest that these matrixes may be useful for a vast range of biotechnological applications based on yeast fermentation.

Selenobaculum gbiensis gen. nov. sp. nov., a new bacterium isolated from the gut microbiota of a patient with Crohn's disease

The human gut microbiota is a complex ecology comprising approximately 10 to 100 trillion microbial cells. Most of the bacteria detected by 16s rRNA sequencing have yet to be cultured, but intensive attempts to isolate the novel bacteria have improved our knowledge of the gut microbiome composition and its roles within human host. In our culturomics study, a novel gram-negative, motile, obligately anaerobic, rod-shaped bacteria, designated as strain ICN-92133T, was isolated from a fecal sample of a 26-year-old patient with Crohn's disease. Based on the 16s rRNA sequence of strain ICN-92133T, the phylogeny analysis placed the strain into the family Selenomonadaceae, showing 93.91% similarity with the closely related Massilibacillus massiliensis strain DSM 102838T. Strain ICN-92133T exhibited a genome size of 2,679,003 bp with a GC content of 35.5% which was predicted to contain 26 potential virulence factors and five antimicrobial resistance genes. In comparative genomic analysis, strain ICN-92133T showed digital DNA-DNA Hybridization and OrthoANI values lower than 21.9% and 71.9% with the closest type strains, respectively. In addition, comparing phenotypic, biochemical, and cellular fatty acids with those of closely related strains revealed the distinctiveness of strain ICN-92133T. Based on the taxonogenomic results, strain ICN-92133T is proposed as a novel species belonging to a new genus. Therefore, we suggest the name of the new genus Selenobaculum gen. nov. within the family Selenomonadaceae and strain ICN-92133T (= KCTC 25622T = JCM 36070T) as a type strain of new species Selenobaculum gbiensis sp. nov.

Describing difficult-to-culture bacteria: Taking a shortcut or investing time to discover something new?

Despite the growing interest in isolating representatives of poorly studied and as-yet-uncultivated bacterial phylogenetic groups, these microorganisms remain difficult objects for taxonomic studies. The time required for describing one of these fastidious bacteria is commonly measured in several years. What is even more problematic, many routine laboratory tests, which were originally developed for fast-growing and fast-responding microorganisms, are not fully suitable for many environmentally relevant, slow-growing bacteria. Standard techniques used in chemotaxonomic analyses do not identify unique lipids produced by these bacteria. A common practice of preparing taxonomic descriptions that report a minimal set of features to name a newly isolated organism deepens a gap between microbial ecologists and taxonomists. By contrast, investing time in detailed analysis of cell biology and experimental verification of genome-encoded capabilities of newly isolated microorganisms opens a window for novel, unexpected findings, which may shape our ideas about the functional role of these microbes in the environment.

Touching the (almost) untouchable: a minimally invasive workflow for microbiological and biomolecular analyses of cultural heritage objects

Microbiological and biomolecular approaches to cultural heritage research have expanded the established research horizon from the prevalent focus on the cultural objects' conservation and human health protection to the relatively recent applications to provenance inquiry and assessment of environmental impacts in a global context of a changing climate. Standard microbiology and molecular biology methods developed for other materials, specimens, and contexts could, in principle, be applied to cultural heritage research. However, given certain characteristics common to several heritage objects-such as uniqueness, fragility, high value, and restricted access, tailored approaches are required. In addition, samples of heritage objects may yield low microbial biomass, rendering them highly susceptible to cross-contamination. Therefore, dedicated methodology addressing these limitations and operational hurdles is needed. Here, we review the main experimental challenges and propose a standardized workflow to study the microbiome of cultural heritage objects, illustrated by the exploration of bacterial taxa. The methodology was developed targeting the challenging side of the spectrum of cultural heritage objects, such as the delicate written record, while retaining flexibility to adapt and/or upscale it to heritage artifacts of a more robust constitution or larger dimensions. We hope this tailored review and workflow will facilitate the interdisciplinary inquiry and interactions among the cultural heritage research community.

Hydrogen stable isotope probing of lipids demonstrates slow rates of microbial growth in soil

The rate at which microorganisms grow and reproduce is fundamental to our understanding of microbial physiology and ecology. While soil microbiologists routinely quantify soil microbial biomass levels and the growth rates of individual taxa in culture, there is a limited understanding of how quickly microbes actually grow in soil. For this work, we posed the simple question: what are the growth rates of soil microorganisms? In this study, we measure these rates in three distinct soil environments using hydrogen-stable isotope probing of lipids with 2H-enriched water. This technique provides a taxa-agnostic quantification of in situ microbial growth from the degree of 2H enrichment of intact polar lipid compounds ascribed to bacteria and fungi. We find that growth rates in soil are quite slow and correspond to average generation times of 14 to 45 d but are also highly variable at the compound-specific level (4 to 402 d), suggesting differential growth rates among community subsets. We observe that low-biomass microbial communities exhibit more rapid growth rates than high-biomass communities, highlighting that biomass quantity alone does not predict microbial productivity in soil. Furthermore, within a given soil, the rates at which specific lipids are being synthesized do not relate to their quantity, suggesting a general decoupling of microbial abundance and growth in soil microbiomes. More generally, we demonstrate the utility of lipid-stable isotope probing for measuring microbial growth rates in soil and highlight the importance of measuring growth rates to complement more standard analyses of soil microbial communities.

Metabolic Versatility of the Family Halieaceae Revealed by the Genomics of Novel Cultured Isolates

The family Halieaceae (OM60/NOR5 clade) is a gammaproteobacterial group abundant and cosmopolitan in coastal seawaters and plays an important role in response to phytoplankton blooms. However, the ecophysiology of this family remains understudied because of the vast gap between phylogenetic diversity and cultured representatives. Here, using six pure cultured strains isolated from coastal seawaters, we performed in-depth genomic analyses to provide an overview of the phylogeny and metabolic capabilities of this family. The combined analyses of 16S rRNA genes, genome sequences, and functional genes relevant to taxonomy demonstrated that each strain represents a novel species. Notably, two strains belonged to the hitherto-uncultured NOR5-4 and NOR5-12 subclades. Metabolic reconstructions revealed that the six strains likely have aerobic chemo- or photoheterotrophic lifestyles; five of them possess genes for proteorhodopsin or aerobic anoxygenic phototrophy. The presence of blue- or green-tuned proteorhodopsin in Halieaceae suggested their ability to adapt to light conditions varying with depth or coastal-to-open ocean transition. In addition to the genes of anaplerotic CO2 fixation, genes encoding a complete reductive glycine pathway for CO2 fixation were found in three strains. Putative polysaccharide utilization loci were detected in three strains, suggesting the association with phytoplankton blooms. Read mapping of various metagenomes and metatranscriptomes showed that the six strains are widely distributed and transcriptionally active in marine environments. Overall, the six strains genomically characterized in this study expand the phylogenetic and metabolic diversity of Halieaceae and likely serve as a culture resource for investigating the ecophysiological features of this environmentally relevant bacterial group. IMPORTANCE Although the family Halieaceae (OM60/NOR5 clade) is an abundant and cosmopolitan clade widely found in coastal seas and involved in interactions with phytoplankton, a limited number of cultured isolates are available. In this study, we isolated six pure cultured Halieaceae strains from coastal seawaters and performed a comparative physiological and genomic analysis to give insights into the phylogeny and metabolic potential of this family. The cultured strains exhibited diverse metabolic potential by harboring genes for anaplerotic CO2 fixation, proteorhodopsin, and aerobic anoxygenic phototrophy. Polysaccharide utilization loci detected in some of these strains also indicated an association with phytoplankton blooms. The cultivation of novel strains of Halieaceae and their genomic characteristics largely expanded the phylogenetic and metabolic diversity, which is important for future ecophysiological studies.

Here, there and everywhere: Ecology and biology of the Dependentiae phylum

Our view of bacterial diversity has been dramatically impacted by cultivation-independent approaches such as metagenomics and 16S rRNA gene sequencing. Consequently, most bacterial phyla known to date are only documented by the presence of DNA sequences in databases and lack cultivated representatives. This bacterial majority that is yet-to-be cultivated, is forming the 'Microbial Dark Matter', (MDM) a consortium, whose ecology and biology remain largely unexplored. The Candidatus Dependentiae stands as one of many phyla within this MDM, found worldwide in various environments. Genomic evidence suggests ancestral, unusual adaptations of all Ca. Dependentiae to a host dependent lifestyle. In line with this, protists appear to be important for Ca. Dependentiae biology, as revealed by few recent studies, which enabled their growth in laboratory through host cultivation. However, the Ca. Dependentiae still remain to this day a poorly documented phylum. The present review aims to summarize the current knowledge accumulated on this often found, but rarely highlighted, bacterial phylum.

Insights into the Methodological, Biotic and Abiotic Factors Influencing the Characterization of Xylem-Inhabiting Microbial Communities of Olive Trees

Vascular pathogens are the causal agents of some of the most devastating plant diseases in the world, which can cause, under specific conditions, the destruction of entire crops. These plant pathogens activate a range of physiological and immune reactions in the host plant following infection, which may trigger the proliferation of a specific microbiome to combat them by, among others, inhibiting their growth and/or competing for space. Nowadays, it has been demonstrated that the plant microbiome can be modified by transplanting specific members of the microbiome, with exciting results for the control of plant diseases. However, its practical application in agriculture for the control of vascular plant pathogens is hampered by the limited knowledge of the plant endosphere, and, in particular, of the xylem niche. In this review, we present a comprehensive overview of how research on the plant microbiome has evolved during the last decades to unravel the factors and complex interactions that affect the associated microbial communities and their surrounding environment, focusing on the microbial communities inhabiting the xylem vessels of olive trees (Olea europaea subsp. europaea), the most ancient and important woody crop in the Mediterranean Basin. For that purpose, we have highlighted the role of xylem composition and its associated microorganisms in plants by describing the methodological approaches explored to study xylem microbiota, starting from the methods used to extract xylem microbial communities to their assessment by culture-dependent and next-generation sequencing approaches. Additionally, we have categorized some of the key biotic and abiotic factors, such as the host plant niche and genotype, the environment and the infection with vascular pathogens, that can be potential determinants to critically affect olive physiology and health status in a holobiont context (host and its associated organisms). Finally, we have outlined future directions and challenges for xylem microbiome studies based on the recent advances in molecular biology, focusing on metagenomics and culturomics, and bioinformatics network analysis. A better understanding of the xylem olive microbiome will contribute to facilitate the exploration and selection of specific keystone microorganisms that can live in close association with olives under a range of environmental/agronomic conditions. These microorganisms could be ideal targets for the design of microbial consortia that can be applied by endotherapy treatments to prevent or control diseases caused by vascular pathogens or modify the physiology and growth of olive trees.

Detection of Pathogens and Antimicrobial Resistance Genes in Ventilator-Associated Pneumonia by Metagenomic Next-Generation Sequencing Approach

Background

The early identification of pathogens and their antibiotic resistance are essential for the management and treatment of patients affected by ventilator-associated pneumonia (VAP). However, microbiological culture may be time-consuming and has a limited culturability of many potential pathogens. In this study, we developed a rapid nanopore-based metagenomic next-generation sequencing (mNGS) diagnostic assay for detection of VAP pathogens and antimicrobial resistance genes (ARGs).

Patients and Methods

Endotracheal aspirate (ETA) samples from 63 patients with suspected VAP were collected between November 2021 and July 2022. Receiver operating characteristic (ROC) curves were established to compare the pathogen identification performance of the target pathogen reads, reads percent of microbes (RPM) and relative abundance (RA). The evaluation of the accuracy of mNGS was performed comparing with the gold standard and the composite standard, respectively. Then, the ARGs were analyzed by mNGS.

Results

ROC curves showed that RA has the highest diagnostic value and the corresponding threshold was 9.93%. The sensitivity and specificity of mNGS test were 91.3% and 78.3%, respectively, based on the gold standard, while the sensitivity and specificity of mNGS test were 97.4% and 100%, respectively, based on the composite standard. A total of 13 patients were virus-positive based on mNGS results, while the coinfection rate increased from 27% to 46% compared to the rate obtained based on clinical findings. The mNGS test also performed well at predicting antimicrobial resistance phenotypes. Patients with a late-onset VAP had a significantly greater proportion of ARGs in their respiratory microbiome compared to those with early-onset VAP (P = 0.041). Moreover, the median turnaround time of mNGS was 4.43 h, while routine culture was 72.00 h.

Conclusion

In this study, we developed a workflow that can accurately detect VAP pathogens and enable prediction of antimicrobial resistance phenotypes within 5 h of sample receipt by mNGS.

Trait biases in microbial reference genomes

Common culturing techniques and priorities bias our discovery towards specific traits that may not be representative of microbial diversity in nature. So far, these biases have not been systematically examined. To address this gap, here we use 116,884 publicly available metagenome-assembled genomes (MAGs, completeness ≥80%) from 203 surveys worldwide as a culture-independent sample of bacterial and archaeal diversity, and compare these MAGs to the popular RefSeq genome database, which heavily relies on cultures. We compare the distribution of 12,454 KEGG gene orthologs (used as trait proxies) in the MAGs and RefSeq genomes, while controlling for environment type (ocean, soil, lake, bioreactor, human, and other animals). Using statistical modeling, we then determine the conditional probabilities that a species is represented in RefSeq depending on its genetic repertoire. We find that the majority of examined genes are significantly biased for or against in RefSeq. Our systematic estimates of gene prevalences across bacteria and archaea in nature and gene-specific biases in reference genomes constitutes a resource for addressing these issues in the future.

Machine learning-assisted medium optimization revealed the discriminated strategies for improved production of the foreign and native metabolites

The composition of medium components is crucial for achieving the best performance of synthetic construction in genetically engineered cells. Which and how medium components determine the performance, e.g., productivity, remain poorly investigated. To address the questions, a comparative survey with two genetically engineered Escherichia coli strains was performed. As a case study, the strains carried the synthetic pathways for producing the aromatic compounds of 4-aminophenylalanine (4APhe) or tyrosine (Tyr), common in the upstream but differentiated in the downstream metabolism. Bacterial growth and compound production were examined in hundreds of medium combinations that comprised 48 pure chemicals. The resultant data sets linking the medium composition to bacterial growth and production were subjected to machine learning for improved production. Intriguingly, the primary medium components determining the production of 4PheA and Tyr were differentiated, which were the initial resource (glucose) of the synthetic pathway and the inducer (IPTG) of the synthetic construction, respectively. Fine-tuning of the primary component significantly increased the yields of 4APhe and Tyr, indicating that a single component could be crucial for the performance of synthetic construction. Transcriptome analysis observed the local and global changes in gene expression for improved production of 4APhe and Tyr, respectively, revealing divergent metabolic strategies for producing the foreign and native metabolites. The study demonstrated that ML-assisted medium optimization could provide a novel point of view on how to make the synthetic construction meet the designed working principle and achieve the expected biological function.

The Neolithic site "La Marmotta": DNA metabarcoding to identify the microbial deterioration of waterlogged archeological wood

Introduction

The evaluation of biological degradation of waterlogged archeological wood is crucial to choose the conservative and protective treatments to be applied to the wooden material. The waterlogged environmental conditions are characterized by oxygen scarcity, only allowing the growth of adapted microbes capable to degrade the organic wooden material, mainly erosion bacteria and soft-rot fungi. In this work, we characterized and evaluated the biodegradation state and the microbial communities of wooden fragments preserved in storage tanks. These were preserved by waterlogging within the Neolithic village "La Marmotta," currently found under the Bracciano Lake (Lazio, Italy).

Methods

The waterlogged wood samples were first identified taxonomically with an optical microscope, also allowing an evaluation of their preservation state. The microbial community was then evaluated through the sequencing of Internal Transcribed Spacer sequences for fungi and 16S for bacteria with the Oxford Nanopore Technologies (ONT) MinION platform.

Results

The identified microbial community appears to be consistent with the waterlogged samples, as many bacteria attributable to the erosion of wood and ligninolytic fungi have been sequenced.

Discussion

The reported results highlight the first use of targeted metabarcoding by ONT applied to study the biodeterioration of waterlogged archeological wood.

Cross Cultivation on Homologous/Heterologous Plant-Based Culture Media Empowers Host-Specific and Real Time In Vitro Signature of Plant Microbiota

Alliances of microbiota with plants are masked by the inability of in vitro cultivation of their bulk. Pure cultures piled in international centers originated from dissimilar environments/hosts. Reporting that plant root/leaf-based culture media support the organ-specific growth of microbiota, it was of interest to further investigate if a plant-based medium prepared from homologous (maize) supports specific/adapted microbiota compared to another prepared from heterologous plants (sunflower). The culture-independent community of maize phyllosphere was compared to communities cross-cultivated on plant broth-based media: CFU counts and taxa prevalence (PCR-DGGE; Illumina MiSeq amplicon sequencing). Similar to total maize phyllospheric microbiota, culture-dependent communities were overwhelmed by Proteobacteria (>94.3–98.3%); followed by Firmicutes (>1.3–3.7%), Bacteroidetes (>0.01–1.58%) and Actinobacteria (>0.06–0.34%). Differential in vitro growth on homologous versus heterologous plant-media enriched/restricted various taxa. In contrast, homologous cultivation over represented members of Proteobacteria (ca. > 98.0%), mainly Pseudomonadaceae and Moraxellaceae; heterologous cultivation and R2A enriched Firmicutes (ca. > 3.0%). The present strategy simulates/fingerprints the chemical composition of host plants to expand the culturomics of plant microbiota, advance real-time in vitro cultivation and lab-keeping of compatible plant microbiota, and identify preferential pairing of plant-microbe partners toward future synthetic community (SynComs) research and use in agriculture.

SnakeMAGs: a simple, efficient, flexible and scalable workflow to reconstruct prokaryotic genomes from metagenomes

Background: Over the last decade, we have observed in microbial ecology a transition from gene-centric to genome-centric analyses. Indeed, the advent of metagenomics combined with binning methods, single-cell genome sequencing as well as high-throughput cultivation methods have contributed to the continuing and exponential increase of available prokaryotic genomes, which in turn has favored the exploration of microbial metabolisms. In the case of metagenomics, data processing, from raw reads to genome reconstruction, involves various steps and software which can represent a major technical obstacle. Methods: To overcome this challenge, we developed SnakeMAGs, a simple workflow that can process Illumina data, from raw reads to metagenome-assembled genomes (MAGs) classification and relative abundance estimate. It integrates state-of-the-art bioinformatic tools to sequentially perform: quality control of the reads (illumina-utils, Trimmomatic), host sequence removal (optional step, using Bowtie2), assembly (MEGAHIT), binning (MetaBAT2), quality filtering of the bins (CheckM, GUNC), classification of the MAGs (GTDB-Tk) and estimate of their relative abundance (CoverM). Developed with the popular Snakemake workflow management system, it can be deployed on various architectures, from single to multicore and from workstation to computer clusters and grids. It is also flexible since users can easily change parameters and/or add new rules. Results: Using termite gut metagenomic datasets, we showed that SnakeMAGs is slower but allowed the recovery of more MAGs encompassing more diverse phyla compared to another similar workflow named ATLAS. Importantly, these additional MAGs showed no significant difference compared to the other ones in terms of completeness, contamination, genome size nor relative abundance. Conclusions: Overall, it should make the reconstruction of MAGs more accessible to microbiologists. SnakeMAGs as well as test files and an extended tutorial are available at https://github.com/Nachida08/SnakeMAGs.

SnakeMAGs: a simple, efficient, flexible and scalable workflow to reconstruct prokaryotic genomes from metagenomes

Background: Over the last decade, we have observed in microbial ecology a transition from gene-centric to genome-centric analyses. Indeed, the advent of metagenomics combined with binning methods, single-cell genome sequencing as well as high-throughput cultivation methods have contributed to the continuing and exponential increase of available prokaryotic genomes, which in turn has favored the exploration of microbial metabolisms. In the case of metagenomics, data processing, from raw reads to genome reconstruction, involves various steps and software which can represent a major technical obstacle. Methods: To overcome this challenge, we developed SnakeMAGs, a simple workflow that can process Illumina data, from raw reads to metagenome-assembled genomes (MAGs) classification and relative abundance estimate. It integrates state-of-the-art bioinformatic tools to sequentially perform: quality control of the reads (illumina-utils, Trimmomatic), host sequence removal (optional step, using Bowtie2), assembly (MEGAHIT), binning (MetaBAT2), quality filtering of the bins (CheckM), classification of the MAGs (GTDB-Tk) and estimate of their relative abundance (CoverM). Developed with the popular Snakemake workflow management system, it can be deployed on various architectures, from single to multicore and from workstation to computer clusters and grids. It is also flexible since users can easily change parameters and/or add new rules. Results: Using termite gut metagenomic datasets, we showed that SnakeMAGs is slower but allowed the recovery of more MAGs encompassing more diverse phyla compared to another similar workflow named ATLAS. Conclusions: Overall, it should make the reconstruction of MAGs more accessible to microbiologists. SnakeMAGs as well as test files and an extended tutorial are available at https://github.com/Nachida08/SnakeMAGs.

Influence of Geochemistry in the Tropical Hot Springs on Microbial Community Structure and Function

Thermophiles inhabiting high temperatures are considered primitive microorganisms on early Earth. In this regard, several works have demonstrated microbial community composition in geothermal environments. Despite that, studies on hot springs located in the Indian subcontinent viz., Surajkund in the district Hazaribag, Jharkhand; Bakreshwar in the district Birbhum, West Bengal; Tantloi in the district Dumka, and Sidpur in the district Pakur, Jharkhand are scanty. Nonetheless, the metagenomic analysis of these hot springs showed significant differences in the predominant phyla corresponding to geochemical properties. The Chloroflexi, Proteobacteria, Actinobacteria, Deinococcus-Thermus, and Firmicutes were dominant phyla in all the samples. In contrast, Meiothermus was more in comparatively low-temperature hot springs. In addition, archaeal phyla, Euryarchaeota, Candidatus Bathyarchaeota, and Crenarchaeota were predominant in all samples. The canonical correspondence analysis (CCA) showed the abundance of Deinococcus, Thermus, Pyrobaculum, Kocuria, and Geodermatophilus positively correlated with the aqueous concentration of sulfate, fluoride, and argon in relatively high-temperature (≥ 72 °C) hot springs. However, at a lower temperature (≤ 63 °C), Thermodesulfovibrio, Caldilinea, Chloroflexus, Meiothermus, and Tepidimonas are positively correlated with the concentration of zinc, iron, and dissolved oxygen. Further, hierarchical clustering exhibits variations in its functional attributes depending on the temperature gradients. Metagenome analysis predicted carbon, methane, sulfur, and nitrogen metabolism genes, indicating a wide range of bacteria and archaea habitation in these hot springs. In addition, identified several genes encode polyketide biosynthesis pathways. The present study described the microbial community composition and function in the tropical hot springs and their relationship with the environmental variables.

Single-cell-level microfluidics assisted with resuscitation-promoting factor technology (SMART) to isolate novel biphenyl-degrading bacteria from typical soils in eastern China

Soil microorganisms represent one of the largest biodiversity reservoirs. However, most low-abundance, slow-growing or dormant microorganisms in soils are difficult to capture with traditional enrichment culture methods. These types of microorganisms represent a valuable "microbial seed bank". To better exploit and utilize this "microbial dark matter", we developed a novel strategy that integrates single-cell-level isolation with microfluidics technology and culture with resuscitation-promoting factor (Rpf) to isolate biphenyl-degrading bacteria from four typical soils (paddy soil, red soil, alluvial soil and black soil) in eastern China. Multitudinous bacteria were successfully isolated and cultured; some of the identified clades have not been previously linked to biphenyl biodegradation, such as Actinotalea, Curtobacterium and Rothia. Soil microcosmic experiments validated that some bacteria are responsible for biphenyl degradation in soil. In addition, genomic sequencing and Illumina MiSeq sequencing of 16S rRNA genes indicated that exogenous Rpf mainly promotes the recovery and growth of bacteria containing endogenous Rpf-encoding genes. In summary, this study provides a novel strategy for capturing target functional microorganisms in soils, indicates potential bioresources for the bioremediation of contaminated soils, and enhances our current understanding of the mechanisms involved in the response to exogenous Rpf.

Marine Bioprospecting, Biocatalysis and Process Development

Oceans possess tremendous diversity in microbial life. The enzymatic machinery that marine bacteria present is the result of extensive evolution to assist cell survival under the harsh and continuously changing conditions found in the marine environment. Several bacterial cells and enzymes are already used at an industrial scale, but novel biocatalysts are still needed for sustainable industrial applications, with benefits for both public health and the environment. Metagenomic techniques have enabled the discovery of novel biocatalysts, biosynthetic pathways, and microbial identification without their cultivation. However, a key stage for application of novel biocatalysts is the need for rapid evaluation of the feasibility of the bioprocess. Cultivation of not-yet-cultured bacteria is challenging and requires new methodologies to enable growth of the bacteria present in collected environmental samples, but, once a bacterium is isolated, its enzyme activities are easily measured. High-throughput screening techniques have also been used successfully, and innovative in vitro screening platforms to rapidly identify relevant enzymatic activities continue to improve. Small-scale approaches and process integration could improve the study and development of new bioprocesses to produce commercially interesting products. In this work, the latest studies related to (i) the growth of marine bacteria under laboratorial conditions, (ii) screening techniques for bioprospecting, and (iii) bioprocess development using microreactors and miniaturized systems are reviewed and discussed.

Balancing Trade-Offs Imposed by Growth Media and Mass Spectrometry for Bacterial Exometabolomics

The bacterial exometabolome consists of a vast array of specialized metabolites, many of which are only produced in response to specific environmental stimuli. For this reason, it is desirable to control the extracellular environment with a defined growth medium composed of pure ingredients. However, complex (undefined) media are expected to support the robust growth of a greater variety of microorganisms than defined media. Here, we investigate the trade-offs inherent to a range of complex and defined solid media for the growth of soil microorganisms, production of specialized metabolites, and detection of these compounds using direct infusion mass spectrometry. We find that complex media support growth of more soil microorganisms, as well as allowing for the detection of more previously discovered natural products as a fraction of total m/z features detected in each sample. However, the use of complex media often caused mass spectrometer injection failures and poor-quality mass spectra, which in some cases resulted in over a quarter of samples being removed from analysis. Defined media, while more limiting in growth, generated higher quality spectra and yielded more m/z features after background subtraction. These results inform future exometabolomic experiments requiring a medium that supports the robust growth of many soil microorganisms. IMPORTANCE Bacteria are capable of producing and secreting a rich diversity of specialized metabolites. Yet, much of their exometabolome remains hidden due to challenges associated with eliciting specialized metabolite production, labor-intensive sample preparation, and time-consuming analysis techniques. Using our versatile three-dimensional (3D)-printed culturing platform, SubTap, we demonstrate that rapid exometabolomic data collection from a diverse set of environmental bacteria is feasible. We optimized our platform by surveying Streptomyces isolated from soil on a variety of media types to assess viability, degree of specialized metabolite production, and compatibility with downstream LESA-DIMS analysis. Ultimately, this will enable data-rich experimentation, allowing for a better understanding of bacterial exometabolomes.

Culture dependent and independent characterization of endophytic bacteria in the seeds of highland barley

Endophytes in the seeds of plants have shown plant growth promoting (PGP) properties. Highland barley is an economically important crop and a major part of the local diet in the Tibetan Plateau, China, with potential health benefits. We applied culture-dependent and culture-independent methods to study endophytic bacteria in the seeds of eight Highland barley varieties. Based on the seed properties, the variety Ali was clearly separated from the other varieties except the variety CM. Most of the 86 isolates were assigned into genus Bacillus. Approximately half of the isolates showed PGP properties in vitro. Compared to the not-inoculated plants, inoculation with the isolate Bacillus tequilensis LZ-9 resulted in greater length and number of roots, and in bigger aboveground and root weights. Based on the 16S rRNA gene sequencing, the seed microbiome was majorly affiliated with the phylum Proteobacteria and the family Enterobacteriaceae. Overall, the bacterial community compositions in the different varieties were different from each other, yet the between variety differences in community composition seemed relatively small. The differences in community compositions were associated with differences in the total and reducing sugar contents and viscosity of the seeds, thus possibly connected to differences in the osmotic pressure tolerance of the endophytes. The results suggested that the seed endophytes are likely to promote the growth of Highland barley since germination.

MediaDive: the expert-curated cultivation media database

We present MediaDive (https://mediadive.dsmz.de), a comprehensive and expert-curated cultivation media database, which comprises recipes, instructions and molecular compositions of >3200 standardized cultivation media for >40 000 microbial strains from all domains of life. MediaDive is designed to enable broad range applications from every-day-use in research and diagnostic laboratories to knowledge-driven support of new media design and artificial intelligence-driven data mining. It offers a number of intuitive search functions and comparison tools, for example to identify media for related taxonomic groups and to integrate strain-specific modifications. Besides classical PDF archiving and printing, the state-of-the-art website allows paperless use of media recipes on mobile devices for convenient wet-lab use. In addition, data can be retrieved using a RESTful web service for large-scale data analyses. An internal editor interface ensures continuous extension and curation of media by cultivation experts from the Leibniz Institute DSMZ, which is interlinked with the growing microbial collections at DSMZ. External user engagement is covered by a dedicated media builder tool. The standardized and programmatically accessible data will foster new approaches for the design of cultivation media to target the vast majority of uncultured microorganisms.

Microbial Journey: Mount Everest to Mars

A rigorous exploration of microbial diversity has revealed its presence on Earth, deep oceans, and vast space. The presence of microbial life in diverse environmental conditions, ranging from moderate to extreme temperature, pH, salinity, oxygen, radiations, and altitudes, has provided the necessary impetus to search for them by extending the limits of their habitats. Microbiology started as a distinct science in the mid-nineteenth century and has provided inputs for the betterment of mankind during the last 150 years. As beneficial microbes are assets and pathogens are detrimental, studying both have its own merits. Scientists are nowadays working on illustrating the microbial dynamics in Earth's subsurface, deep sea, and polar regions. In addition to studying the role of microbes in the environment, the microbe-host interactions in humans, animals and plants are also unearthing newer insights that can help us to improve the health of the host by modulating the microbiota. Microbes have the potential to remediate persistent organic pollutants. Antimicrobial resistance which is a serious concern can also be tackled only after monitoring the spread of resistant microbes using disciplines of genomics and metagenomics The cognizance of microbiology has reached the top of the world. Space Missions are now looking for signs of life on the planets (specifically Mars), the Moon and beyond them. Among the most potent pieces of evidence to support the existence of life is to look for microbial, plant, and animal fossils. There is also an urgent need to deliberate and communicate these findings to layman and policymakers that would help them to take an adequate decision for better health and the environment around us. Here, we present a glimpse of recent advancements by scientists from around the world, exploring and exploiting microbial diversity.

Competition-cooperation in the chemoautotrophic ecosystem of Movile Cave: first metagenomic approach on sediments

BACKGROUND

Movile Cave (SE Romania) is a chemoautotrophically-based ecosystem fed by hydrogen sulfide-rich groundwater serving as a primary energy source analogous to the deep-sea hydrothermal ecosystems. Our current understanding of Movile Cave microbiology has been confined to the sulfidic water and its proximity, as most studies focused on the water-floating microbial mat and planktonic accumulations likely acting as the primary production powerhouse of this unique subterranean ecosystem. By employing comprehensive genomic-resolved metagenomics, we questioned the spatial variation, chemoautotrophic abilities, ecological interactions and trophic roles of Movile Cave's microbiome thriving beyond the sulfidic-rich water.

RESULTS

A customized bioinformatics pipeline led to the recovery of 106 high-quality metagenome-assembled genomes from 7 cave sediment metagenomes. Assemblies' taxonomy spanned 19 bacterial and three archaeal phyla with Acidobacteriota, Chloroflexota, Proteobacteria, Planctomycetota, Ca. Patescibacteria, Thermoproteota, Methylomirabilota, and Ca. Zixibacteria as prevalent phyla. Functional gene analyses predicted the presence of CO2 fixation, methanotrophy, sulfur and ammonia oxidation in the explored sediments. Species Metabolic Coupling Analysis of metagenome-scale metabolic models revealed the highest competition-cooperation interactions in the sediments collected away from the water. Simulated metabolic interactions indicated autotrophs and methanotrophs as major donors of metabolites in the sediment communities. Cross-feeding dependencies were assumed only towards 'currency' molecules and inorganic compounds (O2, PO43-, H+, Fe2+, Cu2+) in the water proximity sediment, whereas hydrogen sulfide and methanol were assumedly traded exclusively among distant gallery communities.

CONCLUSIONS

These findings suggest that the primary production potential of Movile Cave expands way beyond its hydrothermal waters, enhancing our understanding of the functioning and ecological interactions within chemolithoautotrophically-based subterranean ecosystems.

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.

Differences in Supragingival Microbiome in Patients with and without Full-Crown Prostheses

Objectives: To characterize the microflora profile of supragingival biofilm in patients with and without full-crown prostheses. Methods: Plaque samples of full-crown prostheses and teeth in patients with porcelain-fused-to-metal crowns, all-ceramic crowns, and no prostheses were collected (three patients per group), using 16S rRNA high-throughput sequencing technology to conduct DNA sequencing on the samples and using Qiime, R, and PICRUSt2 software to perform bioinformatics analyses and functional analyses on sequencing data. Results: In total, 110,209 valid sequences were obtained in the experiment, corresponding to 11 phyla and 120 genera. The predominant species shared by the three groups were phyla Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria, and Proteobacteria and genera Rothia, Porphyromonas, Prevotella, Streptococcus, Veillonella, Leptotrichia, Neisseria, Citrobacter, and Pseudomonas. The species-difference analysis showed that genus Hameophilus significantly increased after the patient wore the dental prosthesis. Compared with the no-prosthesis samples, the functional analysis showed that cell motility increased in the samples from full-crown prostheses, while replication and repair, and translation decreased. Conclusions: This study reveals the changes in the oral microbial community of patients with full-crown prostheses, which could provide insights regarding the safety of materials for long-term use in the oral cavity.