Improved culturability of soil bacteria and isolation in pure culture of novel members of the divisions Acidobacteria, Actinobacteria, Proteobacteria, and Verrucomicrobia

Complete genome sequence of potential plant growth-promoting Bacillus altitudinis strain AIMST-CREST03 isolated from paddy field bulk soil

We present the complete genome of a potential plant growth-promoting bacteria Bacillus altitudinis AIMST-CREST03 isolated from a high-yielding paddy plot. The genome is 3,669,202 bp in size with a GC content of 41%. Annotation predicted 3,327 coding sequences, including several genes required for plant growth promotion.

Enhancement of soil aggregation and physical properties through fungal amendments under varying moisture conditions

Soil structure and aggregation are crucial for soil functionality, particularly under drought conditions. Saprobic soil fungi, known for their resilience in low moisture conditions, are recognized for their influence on soil aggregate dynamics. In this study, we explored the potential of fungal amendments to enhance soil aggregation and hydrological properties across different moisture regimes. We used a selection of 29 fungal isolates, recovered from soils treated under drought conditions and varying in colony density and growth rate, for single-strain inoculation into sterilized soil microcosms under either low or high moisture (≤-0.96 and -0.03 MPa, respectively). After 8 weeks, we assessed soil aggregate formation and stability, along with soil properties such as soil water content, water hydrophobicity, sorptivity, total fungal biomass and water potential. Our findings indicate that fungal inoculation altered soil hydrological properties and improved soil aggregation, with effects varying based on the fungal strains and soil moisture levels. We found a positive correlation between fungal biomass and enhanced soil aggregate formation and stabilization, achieved by connecting soil particles via hyphae and modifying soil aggregate sorptivity. The improvement in soil water potential was observed only when the initial moisture level was not critical for fungal activity. Overall, our results highlight the potential of using fungal inoculation to improve the structure of agricultural soil under drought conditions, thereby introducing new possibilities for soil management in the context of climate change.

Soil bacteria and fungi communities are shaped by elevation influences in Colombian forest and páramo natural ecosystems

The influence of elevation on natural terrestrial ecosystems determines the arrangements of microbial communities in soils to be associated with biotic and abiotic factors. To evaluate changes of fungi and bacteria at the community level along an elevational gradient (between 1000 and 3800 m.a.s.l.), physicochemical measurements of soils, taxonomic identifications of plants, and metabarcoding sequences of the 16S rRNA gene for bacteria and the ITS1 region for fungi were obtained. The bacterial taxonomic composition showed that Acidobacteriota increased in abundance with elevation, while Actinobacteriota and Verrucomicrobiota decreased. Furthermore, Firmicutes and Proteobacteria maintained maximum levels of abundance at intermediate elevations (1200 and 2400 m.a.s.l.). In fungi, Ascomycota was more abundant at higher elevations, Basidiomycota tended to dominate at lower elevations, and Mortierellomycota had a greater presence at intermediate sites. These results correlated with the edaphic parameters of decreasing pH and increasing organic carbon and available nitrogen with elevation. In addition, the Shannon index found a greater diversity in bacteria than fungi, but both showed a unimodal pattern with maximum values in the Andean Forest at 2400 m.a.s.l. Through the microbial characterization of the ecosystems, the elevational gradient, soil properties, and vegetation were found to exert significant effects on microbial communities and alpha diversity indices. We conclude that the most abundant soil microorganisms at the sampling points differed in abundance and diversity according to the variations in factors influencing ecological communities.

Buffer-free CAS assay using a diluted growth medium efficiently detects siderophore production and microbial growth

Siderophores are iron chelators and low-molecular-weight compounds secreted by various microorganisms under low-iron conditions. Many microorganisms produce siderophores in the natural environment as iron is an essential element for many of them. CAS assays are widely used to detect siderophores in cultures of various microorganisms; however, it is necessary to improve their sensitivity for the efficient application to fastidious microorganisms. We developed a simple, high-throughput CAS assay employing a buffer-free CAS reagent and diluted growth medium (10% dR2A) in a 96-well microplate. Using a diluted growth medium in agar plates suitable for iron-restricted conditions supported siderophore production by microorganisms from activated sludge. A buffer-free CAS reagent combined with a diluted growth medium revealed that these microorganisms tended to produce more siderophores or iron chelators than microorganisms under iron-rich conditions. Moreover, this buffer-free CAS assay easily and efficiently detected not only siderophore production but also the growth of fastidious microorganisms.

Diversity and plant growth promoting ability of rice root-associated bacteria in Burkina-Faso and cross-comparison with metabarcoding data

Plant-associated bacteria are essential partners in plant health and development. In addition to taking advantage of the rapid advances recently achieved in high-throughput sequencing approaches, studies on plant-microbiome interactions require experiments with culturable bacteria. A study on the rice root microbiome was recently initiated in Burkina Faso. As a follow up, the aim of the present study was to develop a collection of corresponding rice root-associated bacteria covering maximum diversity, to assess the diversity of the obtained isolates based on the culture medium used, and to describe the taxonomy, phenotype and abundance of selected isolates in the rice microbiome. More than 3,000 isolates were obtained using five culture media (TSA, NGN, NFb, PCAT, Baz). The 16S rRNA fragment sequencing of 1,013 selected isolates showed that our working collection covered four bacterial phyla (Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes) and represented 33% of the previously described diversity of the rice root microbiome at the order level. Phenotypic in vitro analysis of the plant growth promoting capacity of the isolates revealed an overall ammonium production and auxin biosynthesis capacity, while siderophore production and phosphate solubilisation were enriched in Burkholderia, Ralstonia, Acinetobacter and Pseudomonas species. Of 45 representative isolates screened for growth promotion on seedlings of two rice cultivars, five showed an ability to improve the growth of both cultivars, while five others were effective on only one cultivar. The best results were obtained with Pseudomonas taiwanensis ABIP 2315 and Azorhizobium caulinodans ABIP 1219, which increased seedling growth by 158% and 47%, respectively. Among the 14 best performing isolates, eight appeared to be abundant in the rice root microbiome dataset from previous study. The findings of this research contribute to the in vitro and in planta PGP capacities description of rice root-associated bacteria and their potential importance for plants by providing, for the first time, insight into their prevalence in the rice root microbiome.

Sterility testing of germ-free mouse colonies

In biomedical research, germ-free and gnotobiotic mouse models enable the mechanistic investigation of microbiota-host interactions and their role on (patho)physiology. Throughout any gnotobiotic experiment, standardized and periodic microbiological testing of defined gnotobiotic housing conditions is a key requirement. Here, we review basic principles of germ-free isolator technology, the suitability of various sterilization methods, and the use of sterility testing methods to monitor germ-free mouse colonies. We also discuss their effectiveness and limitations, and share the experience with protocols used in our facility. In addition, possible sources of isolator contamination are discussed and an overview of reported contaminants is provided.

Microbe combined with Fe2+-heat activated persulfate to decompose phenanthrene in red soil: comparison of acid-resistant degrading microflora and indigenous bacteria

This work is designed to counteract the deficiency of targeted research on the PAHs polluted specific soil, especially when the chemicals extremely denatured it. Phenanthrene-contaminated red soil was treated through two-stage process: persulfate oxidation (on dosages of 3.48%, 5.21%, and 6.94%, combined with Fe2+ and β-cyclodextrin, then heated) followed by biodegradation (indigenous bacteria vs. acid-resistant PAHs-degrading microflora (named ADM)) for 90 days. The dosage of oxidant greatly affected the removal efficiencies, which ranged from 46.78 to 85.34% under different treatment. After undergoing oxidation, the soil pH dropped below 3.0 synchronously and retained relatively strong oxidation state. The indigenous bacteria in red soil showed considerable degradation potential that will not vanish upon the sudden change of soil properties, whose average combined removal reached 95.43%, even higher than subgroups of bioaugmentation, but the population structure showed extremely simplex (Proteobacteria as superior occupied proportion of 91.77% after 90-day rehabilitation). The ADM screened from the coking wastewater was dominated by Klebsiella (75.4%) and Pseudomonas (23.6%), whose cooperation with 6.94% persulfate made the residual PHE reduced to less than 50 mg·kg-1 in about 28 days. High-throughput sequencing analysis showed that the microbial community composition of the ADM applied-group was more abundant in the later stage of remediation. ADM inoculation has the advantages of shortening the restoration period and having a positive impact on the soil micro-ecology.

Enhanced denitrification of the AO-MBBR system used for expressway service area sewage treatment: A new perspective on decentralized wastewater treatment

Decentralized wastewater treatment warrants considerable development in numerous countries and regions. Owing to the unique characteristics of high ammonia nitrogen concentrations and low carbon/nitrogen ratio, nitrogen removal is a key challenge in treating expressway service area sewage. In this study, an anoxic/oxic-moving bed biofilm reactor (A/O-MBBR) and a traditional A/O bioreactor were continuously operated for 115 days and their outcomes were compared to investigate the enhancement effect of carriers on the total nitrogen removal (TN) for expressway service area sewage. Results revealed that A/O-MBBR required lower dissolved oxygen, exhibited higher tolerance toward harsh conditions, and demonstrated better shock load resistance than traditional A/O bioreactor. The TN removal load of A/O-MBBR reached 181.5 g‧N/(m3‧d), which was 15.24% higher than that of the A/O bioreactor. Furthermore, under load shock resistance, the TN removal load of A/O-MBBR still reached 327.0 g‧N/(m3‧d), with a TN removal efficiency of above 80%. Moreover, kinetics demonstrated that the denitrification rate of the A/O-MBBR was 121.9% higher than that of the A/O bioreactor, with the anoxic tank biofilm contributing 60.9% of the total denitrification rate. Community analysis results revealed that the genera OLB8, uncultured_f_Saprospiraceae and OLB12 were the dominant in biofilm loaded on carriers, and OLB8 was the key for enhanced denitrification. FAPROTAX and PICRUSt2 analyses confirmed that more bacteria associated with nitrogen metabolism were enriched by the A/O-MBBR carriers through full denitrification metabolic pathway and dissimilatory nitrate reduction pathway. This study offers a perspective into the development of cost-effective and high-efficiency treatment solutions for expressway service area sewage.

Uncovering the Secrets of Slow-Growing Bacteria in Tropical Savanna Soil Through Isolation and Genomic Analysis

One gram of soil holds ten billion bacteria of thousands of different species, but most remain unknown, and one of the serious issues is intrinsic to slow-growing bacteria. In this study, we aimed to isolate and characterize slow-growing bacteria from Brazilian Cerrado soil. Over a period of 4 weeks, we conducted an incubation process and selected a total of 92 isolates. These isolates, consisting mostly of slow-growing bacteria, have the ability to thrive in low-water conditions and possess features that promote plant growth. To identify the isolated bacteria, we performed 16S rRNA sequencing analysis and found that the slow-growing strains were genetically similar to known bacterial species but also belonged to a novel group of species. The new strains identified were Caballeronia sp., Neobacillus sp., Bradyrhizobium sp., and high GC Gram-positive species. Furthermore, we conducted growth experiments using various culture media and temperature conditions. These experiments revealed an extended lag phase for five strains, indicating their slow growth characteristics. Genomic analysis of these five slow-growing bacteria showed their potential to participate in biogeochemical cycles, metabolize various carbohydrates, encode proteins with a role in promoting plant growth and have biosynthetic potential for secondary metabolites. Taken together, our findings reveal the untapped potential of slow-growing bacteria in tropical savanna soils.

Impact of Elevational Gradients and Chemical Parameters on Changes in Soil Bacterial Diversity Under Semiarid Mountain Region

Elevation gradients, often regarded as "natural experiments or laboratories", can be used to study changes in the distribution of microbial diversity related to changes in environmental conditions that typically occur over small geographical scales. We obtained bacterial sequences using MiSeq sequencing and clustered them into operational taxonomic units (OTUs). The total number of reads obtained by the bacterial 16S rRNA sequencing analysis was 1,090,555, with an average of approximately 45,439 reads per sample collected from various elevations. The current study observed inconsistent bacterial diversity patterns in samples from the lowest to highest elevations. 983 OTUs were found common among all the elevations. The most unique OTUs were found in the soil sample from elevation_2, followed by elevation_1. Soil sample collected at elevation_6 had the least unique OTUs. Actinobacteria, Protobacteria, Chloroflexi were found most abundant bacterial phyla in current study. Ammonium nitrogen (NH4+-N), and total phosphate (TP) are the main factors influencing bacterial diversity at elevations_1. pH was the main factor influencing the bacterial diversity at elevations_2, elevation_3 and elevation_4. Our results provide new visions on forming and maintaining soil microbial diversity along an elevational gradient and have implications for microbial responses to environmental change in semiarid mountain ecosystems.

Philodulcilactobacillus myokoensis gen. nov., sp. nov., a fructophilic, acidophilic, and agar-phobic lactic acid bacterium isolated from fermented vegetable extracts

Lactic acid bacteria are commonly in the fermentation industry and pose potential positive effects on health. In this study, a new lactic acid bacterium was isolated from fermented vegetable extracts in Myoko, Niigata, Japan. This bacterium is fructophilic, acidophilic, and hard to grow on agar medium. The isolate is Gram-stain-positive, non-spore-forming, non-motile, rod-shaped, and catalase-negative. Growth occurred at pH 3.5-5.5, with optimal growth at pH 4.5-5.0. The cells formed colonies on a solid MRS medium with 20% (w/v) sucrose and 0.8% (w/v) gellan gum under anaerobic conditions. The bacterium was able to grow on up to 50% (w/v) sucrose but not on d-glucose. Moreover, 16S rRNA gene sequence analysis revealed that the strain was most closely related to Apilactobacillus ozensis (93.1% sequence similarity). The values of average nucleotide identity, digital DNA-DNA hybridization, average amino acid sequence identity, and amino acid identity of conserved genes were calculated between the isolated strain (type strain is WR16-4T = NBRC 115064T = DSM 112857T) and its phylogenetically closest type strains. The average nucleotide identity values (73.36-78.28%) and DNA-DNA hybridization values (16.3-32.9%) were significantly lower than the threshold values for species boundaries. The average amino acid sequence identity values (53.96-60.88%) were significantly below the threshold boundary of genus demarcation (68%). The amino acid identity of conserved genes values compared to strain WR16-4T were the genera Apilactobacillus, Nicoliella spurrieriana SGEP1_A5T, Acetilactobacillus jinshanensis HSLZ-75T, and Fructilactobacillus were 62.51-63.79%, 62.87%, 62.03%, and 58.00-61.04%, respectively. The 16S rRNA gene and core genome phylogenetic trees suggested that this novel strain was most closely related to the type strain of A. jinshanensis HSLZ-75T. Based on the physiological, morphological, and phenotypical characteristics of strain WR16-4T, we propose its classification as a novel genus, Philodulcilactobacillus myokoensis gen. nov., sp. nov.

Immobilization of arsenic in different contaminated soils by zero-valent iron-embedded biochar: Effect of soil characteristics and treatment conditions

Although zero-valent iron-embedded biochar (ZVI-BC) has been proposed as an effective amendment for arsenic (As)-contaminated soils, the impacts of soil characteristics and treatment conditions on the remediation process remained poorly understood. Herein, the immobilization of As in four As-contaminated soils (i.e., smelting soil, storage soil, agricultural soil, and mining soil) by ZVI-BC under different amendment dosages, cultivation temperatures, and soil moisture contents were investigated. ZVI-BC showed high As immobilization capacity in all four soils via forming the AsFe co-precipitation, and the liable As was reduced by 82.4-97.0 % with a 2 % (w/w) amendment. The higher temperature could raise the concentration of liable As in all four soils, especially for the storage soil, in which liable As at 35 °C was almost 3 times of that at 25 °C after 50-days treatment, because the elevated temperature enhanced the destruction of the generated AsFe coprecipitation as well as the desorption of As in soils. Too much soil moisture was unfavorable for the As immobilization after 50-days treatment. Flooding tended to inhibit the community diversity of As-detoxicated bacteria, e.g., Halomonas, Bryobacter, and Anaerolinea, thus resulting in the release of liable As. According to the correlation analysis, the crucial influencing factor for As immobilization was different in four soils, which was determined by the soil properties and proportion of liable As. Our study indicates that ZVI-BC is an effective amendment for As immobilization under various conditions, and the biogeochemical processes of As-associated Fe minerals determine the As immobilization during amendment.

The Next Generation of Microbial Ecology and Its Importance in Environmental Sustainability

Collectively, we have been reviewers for microbial ecology, genetics and genomics studies that include environmental DNA (eDNA), microbiome studies, and whole bacterial genome biology for Microbial Ecology and other journals for about three decades. Here, we wish to point out trends and point to areas of study that readers, especially those moving into the next generation of microbial ecology research, might learn and consider. In this communication, we are not saying the work currently being accomplished in microbial ecology and restoration biology is inadequate. What we are saying is that a significant milestone in microbial ecology has been reached, and approaches that may have been overlooked or were unable to be completed before should be reconsidered in moving forward into a new more ecological era where restoration of the ecological trajectory of systems has become critical. It is our hope that this introduction, along with the papers that make up this special issue, will address the sense of immediacy and focus needed to move into the next generation of microbial ecology study.

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.

Reaching unreachables: Obstacles and successes of microbial cultivation and their reasons

In terms of the number and diversity of living units, the prokaryotic empire is the most represented form of life on Earth, and yet it is still to a significant degree shrouded in darkness. This microbial "dark matter" hides a great deal of potential in terms of phylogenetically or metabolically diverse microorganisms, and thus it is important to acquire them in pure culture. However, do we know what microorganisms really need for their growth, and what the obstacles are to the cultivation of previously unidentified taxa? Here we review common and sometimes unexpected requirements of environmental microorganisms, especially soil-harbored bacteria, needed for their replication and cultivation. These requirements include resuscitation stimuli, physical and chemical factors aiding cultivation, growth factors, and co-cultivation in a laboratory and natural microbial neighborhood.

Biotechnological methods to remove microplastics: a review

Microplastics pollution is major threat to ecosystems and is impacting abiotic and biotic components. Microplastics are diverse and highly complex contaminants that transport other contaminants and microbes. Current methods to remove microplastics include biodegradation, incineration, landfilling, and recycling. Here we review microplastics with focus on sources, toxicity, and biodegradation. We discuss the role of algae, fungi, bacteria in the biodegradation, and we present biotechnological methods to enhance degradation, e.g., gene editing tools and bioinformatics.

Multispecies Bacterial Bio-Input: Tracking and Plant-Growth-Promoting Effect on Lettuce var. sagess

The use of multispecies bacterial bio-inputs is a promising strategy for sustainable crop production over the use of single-species inoculants. Studies of the use of multispecies bio-inputs in horticultural crops are scarce, not only on the growth-promoting effects of each bacterium within the formulation, but also on their compatibility and persistence in the root environment. In this work, we described that a multispecies bacterial bio-input made up of Azospirillum argentinense Az39, Gluconacetobacter diazotrophicus PAL-5, Pseudomonas protegens Pf-5 and Bacillus sp. Dm-B10 improved lettuce plant growth more effectively than when these strains were inoculated as single-species bio-inputs. Bacteria persisted together (were compatible) and also colonized seedling roots of lettuce plants grown in controlled conditions. Interestingly, colonization was highly related to an early and enhanced growth of seedlings grown in the nursery. A similar effect on plant growth was found in lettuce plants in a commercial greenhouse production in the peri-urban area of La Plata City, Buenos Aires, Argentina. To our knowledge, this is the first study demonstrating that a synthetic mixture of bacteria can colonize and persist on lettuce plants, and also showing their synergistic beneficial effect both in the nursery greenhouse as well as the commercial production farm.

Untangling the Effects of Plant Genotype and Soil Conditions on the Assembly of Bacterial and Fungal Communities in the Rhizosphere of the Wild Andean Blueberry (Vaccinium floribundum Kunth)

Microbial communities in the rhizosphere influence nutrient acquisition and stress tolerance. How abiotic and biotic factors impact the plant microbiome in the wild has not been thoroughly addressed. We studied how plant genotype and soil affect the rhizosphere microbiome of Vaccinium floribundum, an endemic species of the Andean region that has not been domesticated or cultivated. Using high-throughput sequencing of the 16S rRNA and ITS region, we characterized 39 rhizosphere samples of V. floribundum from four plant genetic clusters in two soil regions from the Ecuadorian Highlands. Our results showed that Proteobacteria and Acidobacteria were the most abundant bacterial phyla and that fungal communities were not dominated by any specific taxa. Soil region was the main predictor for bacterial alpha diversity, phosphorous and lead being the most interesting edaphic factors explaining this diversity. The interaction of plant genotype and altitude was the most significant factor associated with fungal diversity. This study highlights how different factors govern the assembly of the rhizosphere microbiome of a wild plant. Bacterial communities depend more on the soil and its mineral content, while plant genetics influence the fungal community makeup. Our work illustrates plant-microbe associations and the drivers of their variation in a unique unexplored ecosystem from the Ecuadorian Andes.

Biodegradation of macro- and micro-plastics in environment: A review on mechanism, toxicity, and future perspectives

Plastic waste has gained remarkable research attention due to its accumulation, associated environmental issues, and impact on living organisms. In order to overcome this challenge, there is an urgent need for its removal from the environment. Under this menace, finding appropriate treatment methods like biodegradation instead of typical treatment methods is of supreme importance. However, there is a limited review on bio-decomposition of plastics, existing microbial species, their degradation efficacy, and mechanism. From this point of view, this study focused on a brief overview of biodegradation such as influencing factors on biodegradation, existing species for macro- and micro-plastics, and present research gap. Degradation percentage, limitations of existing species, and future recommendations are proposed. Microbial species such as bacteria, algae, and fungi have the ability to decompose plastics but they are unable to completely mineralize the plastics. Meanwhile, there is limited knowledge about the involved enzymes in plastics degradation, especially in the case of algae. Bio-decomposition of plastics requires more stringent conditions which are usually feasible for field application. This work will be a reference for new researchers to use this effective strategy for plastic pollution removal.

Microbial strategies for degradation of microplastics generated from COVID-19 healthcare waste

COVID-19 pandemic has led to the generation of massive plastic wastes, comprising of onetime useable gloves, masks, tissues, and other personal protective equipment (PPE). Recommendations for the employ of single-use disposable masks made up of various polymeric materials like polyethylene, polyurethane, polyacrylonitrile, and polypropylene, polystyrene, can have significant aftermath on environmental, human as well as animal health. Improper disposal and handling of healthcare wastes and lack of proper management practices are creating serious health hazards and an extra challenge for the local authorities designated for management of solid waste. Most of the COVID-19 medical wastes generated are now being treated by incineration which generates microplastic particles (MPs), dioxin, furans, and various toxic metals, such as cadmium and lead. Moreover, natural degradation and mechanical abrasion of these wastes can lead to the generation of MPs which cause a serious health risk to living beings. It is a major threat to aquatic lives and gets into foods subsequently jeopardizing global food safety. Moreover, the presence of plastic is also considered a threat owing to the increased carbon emission and poses a profound danger to the global food chain. Degradation of MPs by axenic and mixed culture microorganisms, such as bacteria, fungi, microalgae etc. can be considered an eco-sustainable technique for the mitigation of the microplastic menace. This review primarily deals with the increase in microplastic pollution due to increased use of PPE along with different disinfection methods using chemicals, steam, microwave, autoclave, and incineration which are presently being employed for the treatment of COVID-19 pandemic-related wastes. The biological treatment of the MPs by diverse groups of fungi and bacteria can be an alternative option for the mitigation of microplastic wastes generated from COVID-19 healthcare waste.

A Simple and Effective Method for Solid Medium Cultivation of Strictly Hydrogen- and Sulfur-oxidizing Chemolithoautotrophs Predominant in Deep-‍sea Hydrothermal Fields

Strictly hydrogen- and sulfur-oxidizing chemolithoautotrophic bacteria, particularly members of the phyla Campylobacterota and Aquificota, have a cosmopolitan distribution in deep-sea hydrothermal fields. The successful cultivation of these microorganisms in liquid media has provided insights into their physiological, evolutionary, and ecological characteristics. Notably, recent population genetic studies on Sulfurimonas (Campylobacterota) and Persephonella (Aquificota) revealed geographic separation in their populations. Advances in this field of research are largely dependent on the availability of pure cultures, which demand labor-intensive liquid cultivation procedures, such as dilution-to-extinction, given the longstanding assumption that many strictly or facultatively anaerobic chemolithoautotrophs cannot easily form colonies on solid media. We herein describe a simple and cost-effective approach for cultivating these chemolithoautotrophs on solid media. The results obtained suggest that not only the choice of gelling agent, but also the gas phase composition significantly affect the colony-forming ratio of diverse laboratory strains. The use of gellan gum as a gelling agent combined with high concentrations of H2 and CO2 in a pouch bag promoted the formation of colonies. This contrasted with the absence of colony formation on an agar-solidified medium, in which thiosulfate served as an electron donor, nitrate as an electron acceptor, and bicarbonate as a carbon source, placed in anaerobic jars under an N2 atmosphere. Our method efficiently isolated chemolithoautotrophs from a deep-sea vent sample, underscoring its potential value in research requiring pure cultures of hydrogen- and sulfur-oxidizing chemolithoautotrophs.

The identification of the new species Nitratireductor thuwali sp. nov. reveals the untapped diversity of hydrocarbon-degrading culturable bacteria from the arid mangrove sediments of the Red Sea

Introduction

The geological isolation, lack of freshwater inputs and specific internal water circulations make the Red Sea one of the most extreme-and unique-oceans on the planet. Its high temperature, salinity and oligotrophy, along with the consistent input of hydrocarbons due to its geology (e.g., deep-sea vents) and high oil tankers traffic, create the conditions that can drive and influence the assembly of unique marine (micro)biomes that evolved to cope with these multiple stressors. We hypothesize that mangrove sediments, as a model-specific marine environment of the Red Sea, act as microbial hotspots/reservoirs of such diversity not yet explored and described.

Methods

To test our hypothesis, we combined oligotrophic media to mimic the Red Sea conditions and hydrocarbons as C-source (i.e., crude oil) with long incubation time to allow the cultivation of slow-growing environmentally (rare or uncommon) relevant bacteria.

Results and discussion

This approach reveals the vast diversity of taxonomically novel microbial hydrocarbon degraders within a collection of a few hundred isolates. Among these isolates, we characterized a novel species, Nitratireductor thuwali sp. nov., namely, Nit1536^T. It is an aerobic, heterotrophic, Gram-stain-negative bacterium with optimum growth at 37°C, 8 pH and 4% NaCl, whose genome and physiological analysis confirmed the adaptation to extreme and oligotrophic conditions of the Red Sea mangrove sediments. For instance, Nit1536^T metabolizes different carbon substrates, including straight-chain alkanes and organic acids, and synthesizes compatible solutes to survive in salty mangrove sediments. Our results showed that the Red Sea represent a source of yet unknown novel hydrocarbon degraders adapted to extreme marine conditions, and their discovery and characterization deserve further effort to unlock their biotechnological potential.

Iron Minerals Influence the Assembly of Microbial Communities in a Basaltic Glacial Catchment

The influence of mineralogy on the assembly of microbial communities in glacial environments has been difficult to assess due to complications in isolating mineralogy from other variables. Here we assess the abundance and composition of microbial communities that colonized defined minerals incubated for 12 months in two meltwater streams (N and S) emanating from Kaldalónsjökull (Kal), a basalt-hosted glacier in Iceland. The two streams shared similar meltwater geochemistry as well as bedrock and proglacial sediment elemental compositions. Yet genomic DNA and PCR-amplifiable 16S rRNA genes were detected only in Kal S. The amount of recoverable DNA was highest for hematite incubated in Kal S and the composition of 16S rRNA genes recovered from Kal S sediments was most like those recovered from hematite and magnetite, an effect driven largely by similarities in the relative abundance of the putative hydrogenotrophic iron reducer Rhodoferax. We suggest this is attributable to comminution and weathering reactions involving exposed iron silicate minerals that generate and release hydrogen and Fe(III) that can be coupled to support microbial metabolism in Kaldalónsjökull, and possibly other basaltic habitats. The low abundance of cells in Kal N could be due to low availability of Fe(III) or another substrate.

SynMADE: synthetic microbiota across diverse ecosystems

The past two decades have witnessed rapid advances in engineering individual microbial strains to produce biochemicals and biomaterials. However, engineering microbial consortia has been relatively slow. Using systems and synthetic biology approaches, researchers have been developing tools for engineering complex microbiota. In this opinion article, I discuss future directions and visions regarding developing microbiota as a biomanufacturing host. Specifically, I propose that we can develop the soil microbial community itself as a huge bioreactor. Ultimately, researchers will provide a generalizable system that enables us to understand a microbial consortium's interaction and metabolism on diverse temporal and spatial scales to address global problems, including the climate crisis, food inequality, the issue of waste, and sustainable bioproduction.

Sorghum Allelopathy: Alternative Weed Management Strategy and Its Impact on Mung Bean Productivity and Soil Rhizosphere Properties

Simple Summary

Plants are subjected to a variety of biotic and abiotic stresses, which affect the rhizospheric attributes and limit agricultural crop productivity. To meet the food and energy demands of the future, several diverse approaches are used for achieving more stress-tolerant and climate-flexible crops for sustainable yields. Several organic and inorganic amendments are used to ameliorate these stresses. Crop-mediated modification (crop residues and allelopathic extracts) has great effects on weed management, improving rhizospheric attributes, and ultimately producing the best quality yield. Sorghum crop residues and their allelopathic extract can be used as a nutrient resource to enhance soil and crop productivity through their application. Sorghum-mediated crop modification will support the soil health and environmental sustainability, providing insight into the improvement of crop productivity. This study will help policymakers in modelling and enhancing sustainable crop production.

Abstract

The reduction of herbicide use and herbicide-resistant weeds through allelopathy can be a sustainable strategy to combat the concerns of environmental degradation. Allelopathic crop residues carry great potential both as weed suppressers and soil quality enhancers. The influence of sorghum crop residues and water extracts on the weed population, soil enzyme activities, the microbial community, and mung bean crop productivity was investigated in a two-year experiment at the Student Research Farm, University of Agriculture Faisalabad. The experimental treatments comprised two levels of sorghum water extract (10 and 20 L ha⁻¹) and two residue application rates (4 and 6 t ha⁻¹), and no sorghum water extract and residues were used as the control. The results indicated that the incorporation of sorghum water extract and residue resulted in significant changes in weed dynamics and the soil quality indices. Significant reduction in weed density (62%) and in the dry weight of weeds (65%) was observed in T₅. After the harvest, better soil quality indices in terms of the microbial population (72–90%) and microbial activity (32–50%) were observed in the rhizosphere (0–15 cm) by the same treatment. After cropping, improved soil properties in terms of available potassium, available phosphorus soil organic matter, and total nitrogen were higher after the treatment of residue was incorporated, i.e., 52–65%, 29–45%, 62–84%, and 59–91%, respectively. In the case of soil enzymes, alkaline phosphatase and dehydrogenase levels in the soil were 35–41% and 52–77% higher, respectively. However, residue incorporation at 6 t ha⁻¹ had the greatest effect in improving the soil quality indices, mung bean productivity, and reduction of weed density. In conclusion, the incorporation of 6 t ha⁻¹ sorghum residues may be opted to improve soil quality indices, suppress weeds, harvest a better seed yield (37%), and achieve higher profitability (306 $ ha⁻¹) by weed suppression, yield, and rhizospheric properties of spring-planted mung beans. This strategy can provide a probable substitute for instigating sustainable weed control and significant improvement of soil properties in the mung bean crop, which can be a part of eco-friendly and sustainable agriculture.

An activity-based probe targeting the streptococcal virulence factor C5a peptidase

Development of profiling strategies to provide high resolution understanding of enzymes involved in bacterial infections remains an important need. These strategies help resolve enzyme mechanisms of actions and can guide therapeutic development. We have developed a selective new activity-based probe (ABP) targeting a highly conserved surface bound enzyme, C5a peptidase, present in several pathogenic Streptococci. We demonstrate our probe inhibits C5a peptidase activity and enables detection of C5a peptidase expressing pathogens in microbial mixtures. Our profiling strategy selectively labels the pathogen by phenotype and enables specific isolation of the live bacteria providing a route for further in-depth investigation. This study paves the way towards a rapid detection, isolation, and characterization pipeline for existing and emerging strains of most common pathogenic Streptococci.

Soil substrate culturing approaches recover diverse members of Actinomycetota from desert soils of Herring Island, East Antarctica

Antimicrobial resistance is an escalating health crisis requiring urgent action. Most antimicrobials are natural products (NPs) sourced from Actinomycetota, particularly the Streptomyces. Underexplored and extreme environments are predicted to harbour novel microorganisms with the capacity to synthesise unique metabolites. Herring Island is a barren and rocky cold desert in East Antarctica, remote from anthropogenic impact. We aimed to recover rare and cold-adapted NP-producing bacteria, by employing two culturing methods which mimic the natural environment: direct soil culturing and the soil substrate membrane system. First, we analysed 16S rRNA gene amplicon sequencing data from 18 Herring Island soils and selected the soil sample with the highest Actinomycetota relative abundance (78%) for culturing experiments. We isolated 166 strains across three phyla, including novel and rare strains, with 94% of strains belonging to the Actinomycetota. These strains encompassed thirty-five ‘species’ groups, 18 of which were composed of Streptomyces strains. We screened representative strains for genes which encode polyketide synthases and non-ribosomal peptide synthetases, indicating that 69% have the capacity to synthesise polyketide and non-ribosomal peptide NPs. Fourteen Streptomyces strains displayed antimicrobial activity against selected bacterial and yeast pathogens using an in situ assay. Our results confirm that the cold-adapted bacteria of the harsh East Antarctic deserts are worthy targets in the search for bioactive compounds.

Microflora communities which can convert digested sludge to biogas

In the present study, we developed several microflora communities that utilize digested sludge (DS), the recalcitrant waste product of anaerobic digestion, as a substrate for biogas production with the aim of their future application to DS recycling. Strict enrichment with DS as the sole nutrient source was introduced to culture microbes from soil and herbivore dung samples; microflora communities promoting stable levels of biogas production were obtained. The average methane and hydrogen yield from soil-derived microflora were 4.86 and 0.94 ml per 1.0 g DS, respectively. Notably, two microflora communities enriched from a riverbank sediment produced 20.79 ml and 14.10 ml methane from 1.0 g DS. By contrast, the methane and hydrogen yield for herbivore dung-derived microfloras were on average 1.31 ml and 1.87 ml per 1.0 g DS, respectively. Potent hydrogen-biogas producers were obtained from rabbit (4.12 ml per 1.0 g DS), goat (3.16 ml per 1.0 g DS), and sheep dung (2.52 ml per 1.0 g DS). The cultured microflora communities included representatives from the eubacterial genera, Clostridiaceae and Eubacteriaceae together with several anaerobic genera. Pseudomonas spp. are found in the riverbank sediment-derived microfloras, suggesting that the floras employ syntrophic acetate oxidation and hydrogentrophic methanogenesis (SAO-HM) pathway for methane production. The methanogenic microflora communities were dominated by bacteria from the Methanobacteriaceae family and unclassified archaea. Moreover, ascomycetous fungi and protists were found, implying that they act as oxygen scavengers and bacterial grazers, respectively. Enzymatic analysis suggested that the microfloras hydrolyze DS via cellulase, chitinase, and protease activities.

Strategies to access biosynthetic novelty in bacterial genomes for drug discovery

Bacteria provide a rich source of natural products with potential therapeutic applications, such as novel antibiotic classes or anticancer drugs. Bioactivity-guided screening of bacterial extracts and characterization of biosynthetic pathways for drug discovery is now complemented by the availability of large (meta)genomic collections, placing researchers into the postgenomic, big-data era. The progress in next-generation sequencing and the rise of powerful computational tools provide unprecedented insights into unexplored taxa, ecological niches and 'biosynthetic dark matter', revealing diverse and chemically distinct natural products in previously unstudied bacteria. In this Review, we discuss such sources of new chemical entities and the implications for drug discovery with a particular focus on the strategies that have emerged in recent years to identify and access novelty.

Influence of 16S rRNA reference databases in amplicon-based environmental microbiome research

PURPOSE

The reference databases play a pivotal role in amplicon microbiome research, however these databases differ in the sequence content and taxonomic information available. Studies on mock community and human health microbiome have revealed the problems associated with the choice of reference database on the outcome. Nonetheless, the influence of reference databases in environmental microbiome studies is not explicitly illustrated.

METHODS

This study analyzed the amplicon (V1V3, V3V4, V4V5 and V6V8) data of 128 soil samples and evaluated the impact of 16S rRNA databases, Genome Taxonomy Database (GTDB), Ribosomal Database Project (RDP), SILVA and Consensus Taxonomy (ConTax), on microbiome inference.

RESULTS

The analyses showed that the distribution of observed amplicon sequence variants was significantly different (P-value < 2.647e-12) across four datasets, generated using different databases for each amplicon region. In addition, the beta diversity was also found to be altered by different databases. Further investigation revealed that the microbiome composition inferred by various databases differ significantly (P-value = 0.001), irrespective of amplicon regions. This study, found that the core-microbiome structure in environmental studies is influenced by the type of reference database used.

CONCLUSION

In summary, this present study illustrates that the choice of reference database could influence the outcome of environmental microbiome research.

A three-dimensional (3D) printing approach to fabricate an isolation chip for high throughput in situ cultivation of environmental microbes

The full plethora of environmental bacteria is often poorly represented in vitro as the majority remain difficult, if not impossible, to culture under standard laboratory settings. These bacteria often require native conditions for the formation of cell masses that collectively have higher chances of survival. With that, a 3D-printed version of the isolation chip (iChip) was used to cultivate bacteria from a tropical peat swamp in situ prior to growth and maintenance in vitro. Briefly, plates made from either acrylonitrile butadiene styrene (ABS), polylactic acid (PLA), or epoxy resin were tested in terms of their usability and durability under acidic conditions similar to those of peat matter. The epoxy resin plates were then found to be most optimal for the sampling conditions. Peat soil samples were collected from the base of a Koompassia malaccensis tree and reconstituted in molten 10% (wt/vol) tryptone soy agar (TSA) prior to inoculation. The iChips were subsequently assembled and buried in the site of origin. As a comparison, bacteria from the same soil sample were cultivated directly on TSA and incubated at 28 °C for two weeks. Thereafter, agar plugs from the iChip were transferred to TSA plates to allow microcolonies within each plug to grow. Each pure isolate from both cultivation approaches that grew was then pooled and extracted for total DNA prior to 16S rRNA gene amplification and sequencing via Illumina MiSeq. Taxonomic abundance comparison revealed that the bacterial taxa at the level of order were significantly different between the two approaches, particularly in the orders, Burkholderiales, Xanthomonodales, Enterobacteriales, and Actinomycetales (differences of 12.0, 7.1, 8.0, and 4.2%, respectively). This indicated that the 3D-printed iChips present a possible low-cost tool for the isolation of bacterial genera that may not be able to grow on media directly in vitro.

OUP accepted manuscript

Ammonia-oxidising archaea (AOA) are environmentally important microorganisms involved in the biogeochemical cycling of nitrogen. Routine cultivation of AOA is exclusively performed in liquid cultures and reports on their growth on solid medium are scarce. The ability to grow AOA on solid medium would be beneficial for not only the purification of enrichment cultures but also for developing genetic tools. The aim of this study was to develop a reliable method for growing individual colonies from AOA cultures on solid medium. Three phylogenetically distinct AOA strains were tested: ‘Candidatus Nitrosocosmicus franklandus C13’, Nitrososphaera viennensis EN76 and ‘Candidatus Nitrosotalea sinensis Nd2’. Of the gelling agents tested, agar and Bacto-agar severely inhibited growth of all three strains. In contrast, both ‘Ca. N. franklandus C13’ and N. viennensis EN76 tolerated Phytagel™ while the acidophilic ‘Ca. N. sinensis Nd2’ was completely inhibited. Based on these observations, we developed a Liquid-Solid (LS) method that involves immobilising cells in Phytagel™ and overlaying with liquid medium. This approach resulted in the development of visible distinct colonies from ‘Ca. N. franklandus C13’ and N. viennensis EN76 cultures and lays the groundwork for the genetic manipulation of this group of microorganisms.

Tissue-specific diversity of bacterial endophytes in Mexican husk tomato plants (Physalis ixocarpa Brot. ex Horm.), and screening for their multiple plant growth-promoting activities

•

Endophytic bacterial diversity of root, stem, and leaf tissues of Physalis ixocarpa was deciphered.

•

Unique and shared species were found for each plant compartment analyzed.

•

Extensive screening of various isolates exhibited antagonism against fungal pathogens.

•

Diverse endophytes stimulated the growth of Physalis ixocarpa seedlings.

•

Neobacillus drentensis CH23 stood out as an excellent plant growth-promoting bacterium.

The endophytic bacterial diversity of root, stem, and leaf tissues of Mexican husk tomato plants (Physalis ixocarpa) was compared and deciphered, and screened for their plant growth-promoting activity and antagonism against fungal phytopathogens. Total 315 isolates (108 roots, 102 stems, and 105 leaves) were obtained and characterized by 16S ribosomal gene sequencing. The most abundant genera were Bacillus, Microbacterium, Pseudomonas, and Stenotrophomonas. Unique species were found for each tissue analyzed, along with B. thuringiensis, B. toyonensis, Neobacillus drentensis, Paenibacillus castaneae, P. fluorescens, P. poae, and S. maltophilia present throughout the plant. Biodiversity indices did not show significant differences, but root tissues showed the highest abundance of bacterial endophytes. Several isolates showed excellent promotion activities in Physalis ixocarpa seedlings, increasing the length and weight of the root, total biomass, and chlorophyll content. Various isolates also exhibited antagonism against fungal pathogens. Among screened isolates, Neobacillus drentensis CH23 was found in all plant compartments, exhibiting growth-promoting activity and fungal antagonism. Strain CH23 and other endophytes showed the production of indoleacetic acid, siderophores, proteases, and solubilization of phosphates. These results demonstrate that the husk tomato plant endobiome has a high potential as a bioinoculating agent for agriculturally important crops.

Bacteria Cultivated From Sponges and Bacteria Not Yet Cultivated From Sponges-A Review

The application of high-throughput microbial community profiling as well as "omics" approaches unveiled high diversity and host-specificity of bacteria associated with marine sponges, which are renowned for their wide range of bioactive natural products. However, exploration and exploitation of bioactive compounds from sponge-associated bacteria have been limited because the majority of the bacteria remains recalcitrant to cultivation. In this review, we (i) discuss recent/novel cultivation techniques that have been used to isolate sponge-associated bacteria, (ii) provide an overview of bacteria isolated from sponges until 2017 and the associated culture conditions and identify the bacteria not yet cultured from sponges, and (iii) outline promising cultivation strategies for cultivating the uncultivated majority of bacteria from sponges in the future. Despite intensive cultivation attempts, the diversity of bacteria obtained through cultivation remains much lower than that seen through cultivation-independent methods, which is particularly noticeable for those taxa that were previously marked as "sponge-specific" and "sponge-enriched." This poses an urgent need for more efficient cultivation methods. Refining cultivation media and conditions based on information obtained from metagenomic datasets and cultivation under simulated natural conditions are the most promising strategies to isolate the most wanted sponge-associated bacteria.

Comparative Analysis of the Cultured and Total Bacterial Community in the Wheat Rhizosphere Microbiome Using Culture-Dependent and Culture-Independent Approaches

Rhizosphere and root-associated bacteria are key components of crop production and sustainable agriculture. However, utilization of these beneficial bacteria is often limited by conventional culture techniques because a majority of soil microorganisms cannot be cultured using standard laboratory media. Therefore, the purpose of this study was to improve culturability and investigate the diversity of the bacterial communities from the wheat rhizosphere microbiome collected from three locations in Egypt with contrasting soil characteristics by using metagenomic analysis and improved culture-based methods. The improved strategies of the culture-dependent approach included replacing the agar in the medium with gellan gums and modifying its preparation by autoclaving the phosphate and gelling agents separately. Compared to the total operational taxonomic units (OTUs) observed from the metagenomic data sets derived from the three analyzed soils, 1.86 to 2.52% of the bacteria were recovered using the modified cultivation strategies, whereas less than 1% were obtained employing the standard cultivation protocols. Twenty-one percent of the cultivable isolates exhibited multiple plant growth-promoting (PGP) properties, including P solubilization activity and siderophore production. From the metagenomic analysis, the most abundant phyla were Proteobacteria, Actinobacteria, Chloroflexi, Bacteroidetes, and Firmicutes. Moreover, the relative abundance of the specific bacterial taxa was correlated with the soil characteristics, demonstrating the effect of the soil in modulating the plant rhizosphere microbiome.

IMPORTANCE Bacteria colonizing the rhizosphere, a narrow zone of soil surrounding the root system, are known to have beneficial effects in improving the growth and stress tolerance of plants. However, most bacteria in natural environments, especially those in rhizosphere soils, are recalcitrant to cultivation using traditional techniques, and thus their roles in soil health and plant growth remain unexplored. Hence, investigating new culture media and culture conditions to bring “not-yet-cultured” species into cultivation and to identify new functions is still an important task for all microbiologists. To this end, we describe improved cultivation protocols that increase the number and diversity of cultured bacteria from the rhizosphere of wheat plants. Using such approaches will lead to new insights into culturing more beneficial bacteria that live in the plant rhizosphere, in so doing creating greater opportunities not only for field application but also for promoting sustainability.

Bioresource Nutrient Recycling in the Rice-Wheat Cropping System: Cornerstone of Organic Agriculture

This study evaluated the impact of conventional practices (fertilizer alone) and diverse farming approaches (such as green manuring, farmyard manure application, rice-residue incorporation, residue mulching, residue removal and residue burning) on soil attributes. A total of thirty-five farm sites were selected, with five sites (replications) for each farming approach system, which were used over the past three years in the study farms. Characterization of rice residues of all cultivars, green manure crop (sesbenia: Sesbania sesban) and decomposed farmyard manure samples showed differential behaviours for macronutrients and micronutrients. Continuous application of inorganic fertilizers significantly influenced soil attributes, especially electrical conductivity, nutrient contents, bacterial and fungal population and soil enzymatic attributes. The crop residue treatments favourably influenced the soil parameters over the control. Crop residue incorporation or burning significantly increased soil available potassium, microbial biomass, enzymatic activities and organic carbon when compared with applications of chemical fertilizer alone, while total nitrogen content was increased by residue incorporation. However, green manuring and farmyard manure applications showed inferior responses compared with residue management treatment. It is therefore recommended that bioresources should be managed properly to warrant improvements in soil properties, nutrient recycling and the sustainability for crop productivity, in order to achieve sustainable development goals for climate action.

Recent trend, biases and limitations of cultivation-based diversity studies of microbes

The current study attempts to analyze recent trends, biases and limitations of cultivation-based microbial diversity studies based on published, novel species in the past 6 years in the International Journal of Systematic and Evolutionary Microbiology (IJSEM), an official publication of the International Committee on Systematics of Prokaryotes (ICSP) and the Bacteriology and Applied Microbiology (BAM) Division of the International Union of Microbiological Societies (IUMS). IJSEM deals with taxa that have validly published names under the International Code of Nomenclature of Prokaryotes (ICNP). All the relevant publications from the last 6 years were retrieved, sorted and analyzed to get the answers to What is the current rate of novel species description? Which country has contributed substantially and which phyla represented better in culturable diversity studies? What are the current limitations? Published data for the past 6 years indicate that 500-900 novel species are reported annually. China, Korea, Germany, UK, India and the USA are at the forefront while contributions from other nations are meager. Despite the recent development in culturomics tools the dominance of Proteobacteria, Bacteroidetes and Actinobacteria are still prevalent in cultivation, while the representation of archaea, obligate anaerobes, microaerophiles, synergistic symbionts, aerotolerant and other fastidious microbes is poor. Single strain-based taxonomic descriptions prevail and emphasis on objective-based cultivation for biotechnological and environmental significance is not yet conspicuous.

Easy detection of siderophore production in diluted growth media using an improved CAS reagent

Siderophores are low molecular weight organic compounds produced by various microorganisms, especially pathogenic bacteria including rhizobacteria, and have a high affinity for iron. Although most microorganisms are thought to secrete siderophores under iron-depleted conditions, it is unclear how many microorganisms produce siderophores in the natural environment. Also, the chrome azurol sulfonate (CAS) assay, which is widely used for the detection of siderophores, needs to be improved for wider applicability. We developed a simple, high-throughput CAS assay in a 96-well microplate with a concentrated CAS reagent and commonly used diluted growth media in the absence of artificial iron depletion. The improved microplate CAS shuttle assay revealed that it could easily detect siderophores released from Pseudomonas (P.) fluorescence, P. putida, Burlkholderia stabilis, and Ottowia oryzae, as models of siderophore-producing bacteria. This CAS shuttle assay employed along with diluted growth media is a promising tool to screen new siderophore-producing bacteria.

Spatial Variability of Microbial Communities and Salt Distributions Across a Latitudinal Aridity Gradient in the Atacama Desert

Over the past 150 million years, the Chilean Atacama Desert has been transformed into one of the most inhospitable landscapes by geophysical changes, which makes it an ideal Mars analog that has been explored for decades. However, a heavy rainfall that occurred in the Atacama in 2017 provides a unique opportunity to study the response of resident extremophiles to rapid environmental change associated with excessive water and salt shock. Here we combine mineral/salt composition measurements, amendment cell culture experiments, and next-generation sequencing analyses to study the variations in salts and microbial communities along a latitudinal aridity gradient of the Atacama Desert. In addition, we examine the reshuffling of Atacama microbiomes after the rainfall event. Analysis of microbial community composition revealed that soils within the southern arid desert were consistently dominated by Actinobacteria, Chloroflexi, Proteobacteria, Firmicutes, Bacteroidetes, Gemmatimonadetes, Planctomycetes, and Acidobacteria, and Verrucomicrobia. Intriguingly, the hyperarid microbial consortia exhibited a similar pattern to the more southern desert. Salts at the shallow subsurface were dissolved and leached down to a deeper layer, challenging indigenous microorganisms with the increasing osmotic stress. Microbial viability was found to change with aridity and rainfall events. This study sheds light on the structure of xerotolerant, halotolerant, and radioresistant microbiomes from the hyperarid northern desert to the less arid southern transition region, as well as their response to changes in water availability.

The Application of High-Throughput Technologies for the Study of Microbiome and Cancer

Human gut microbiome research, especially gut microbiome, has been developing at a considerable pace over the last decades, driven by a rapid technological advancement. The emergence of high-throughput technologies, such as genomics, transcriptomics, and others, has afforded the generation of large volumes of data, and in relation to specific pathologies such as different cancer types. The current review identifies high-throughput technologies as they have been implemented in the study of microbiome and cancer. Four main thematic areas have emerged: the characterization of microbial diversity and composition, microbial functional analyses, biomarker prediction, and, lastly, potential therapeutic applications. The majority of studies identified focus on the microbiome diversity characterization, which is reaching technological maturity, while the remaining three thematic areas could be described as emerging.

The Role of Gene Duplication in the Divergence of Enzyme Function: A Comparative Approach

Gene duplication is a crucial process involved in the appearance of new genes and functions. It is thought to have played a major role in the growth of enzyme families and the expansion of metabolism at the biosphere's dawn and in recent times. Here, we analyzed paralogous enzyme content within each of the seven enzymatic classes for a representative sample of prokaryotes by a comparative approach. We found a high ratio of paralogs for three enzymatic classes: oxidoreductases, isomerases, and translocases, and within each of them, most of the paralogs belong to only a few subclasses. Our results suggest an intricate scenario for the evolution of prokaryotic enzymes, involving different fates for duplicated enzymes fixed in the genome, where around 20-40% of prokaryotic enzymes have paralogs. Intracellular organisms have a lesser ratio of duplicated enzymes, whereas free-living enzymes show the highest ratios. We also found that phylogenetically close phyla and some unrelated but with the same lifestyle share similar genomic and biochemical traits, which ultimately support the idea that gene duplication is associated with environmental adaptation.

Identifying Hidden Viable Bacterial Taxa in Tropical Forest Soils Using Amplicon Sequencing of Enrichment Cultures

Simple Summary

The study of a microbial community nowadays mostly relies on environmental DNA (eDNA)-based amplicon sequencing. However, some studies report that this method is not able to capture all bacterial taxa in the community. This study presents an enrichment culture-based amplicon sequencing method to estimate the proportion of culturable bacteria in soil. A bacterial community derived from this method was compared with those derived from culture-independent methods (eDNA-based amplicon sequencing). This study revealed that the majority of cultured bacteria were rare or completely absent in the community detected by the culture-independent method. Nevertheless, the dominant bacterial Operational Taxonomic Units (OTUs) were also observed, as 8 out of the 30 most frequently detected bacteria from eDNA were found in the enrichment cultures. The method proposed in this study could extend bacterial community’s information derived from the culture-independent method. Furthermore, the enrichment culture-based amplicon sequencing method could be a promising tool for quick screening of a culturable bacterial community and its associated function for various applications.

Abstract

This study aims to estimate the proportion and diversity of soil bacteria derived from eDNA-based and culture-based methods. Specifically, we used Illumina Miseq to sequence and characterize the bacterial communities from (i) DNA extracted directly from forest soil and (ii) DNA extracted from a mixture of bacterial colonies obtained by enrichment cultures on agar plates of the same forest soil samples. The amplicon sequencing of enrichment cultures allowed us to rapidly screen a culturable community in an environmental sample. In comparison with an eDNA community (based on a 97% sequence similarity threshold), the fact that enrichment cultures could capture both rare and abundant bacterial taxa in forest soil samples was demonstrated. Enrichment culture and eDNA communities shared 2% of OTUs detected in total community, whereas 88% of enrichment cultures community (15% of total community) could not be detected by eDNA. The enrichment culture-based methods observed 17% of the bacteria in total community. FAPROTAX functional prediction showed that the rare and unique taxa, which were detected with the enrichment cultures, have potential to perform important functions in soil systems. We suggest that enrichment culture-based amplicon sequencing could be a beneficial approach to evaluate a cultured bacterial community. Combining this approach together with the eDNA method could provide more comprehensive information of a bacterial community. We expected that more unique cultured taxa could be detected if further studies used both selective and non-selective culture media to enrich bacteria at the first step.

Application of in situ cultivation in marine microbial resource mining

Microbial communities in marine habitats are regarded as underexplored reservoirs for discovering new natural products with potential application. However, only a few microbes in nature can be cultivated in the laboratory. This has led to the development of a variety of isolation and cultivation methods, and in situ cultivation is one of the most popular. Diverse in situ cultivation methods, with the same basic principle, have been applied to a variety of environmental samples. Compared with conventional approaches, these new methods are able to cultivate previously uncultured and phylogenetically novel microbes, many with biotechnological potential. This review introduces the various in situ cultivation methods for the isolation of previously uncultured microbial species and their potential for marine microbial resource mining. Furthermore, studies that investigated the key and previously unidentified mechanisms of growing uncultivated microorganisms by in situ cultivation, which will shed light on the understanding of microbial uncultivability, were also reviewed.

Accessing previously uncultured marine microbial resources by a combination of alternative cultivation methods

Few microbes can grow under laboratory conditions, highlighting the fact that the majority of microbes in environment are still uncultured and untapped resources. This study used alternative cultivation methods, diffusion chambers (DC), dilution-to-extinction culture (DTE) and modified agar preparation step (PS media) to cultivate previously uncultured marine bacterial species. These methods were applied to samples from a coastal intertidal zone, and the results were compared with those from standard direct plating (SDP) cultivation. Among the strains isolated with DC, DTE and PS media methods, 28%, 48% and 33% were novel species, respectively, while the SDP method resulted in the isolation of only 9% of novel species. Most isolates were unique to the method used for their cultivation. This implies that each method is selective in its own way, which is different from SDP, thus able to access species that are difficult to obtain using conventional approaches. Comparing the diversity showed that 75 genera were recovered by the alternative methods, 2.7 times higher than that of the SDP cultivation, which constituted 45% of total diversity from culture-independent sequencing. We conclude that combining alternative cultivation methods represents a highly promising key for accessing 'microbial dark matter'.

Diluted Luria-Bertani medium vs. sewage sludge as growth media: comparison of community structure and diversity in the culturable bacteria

Because colony formation is essential to seek bacterial functions by the direct observation of phenotype, the diversification of colony formation for culturable bacteria is a big challenge in the research field of Environmental Biotechnology. In this study, the biodiversity of cultivable bacteria (colony or liquid culture) was compared by using Luria-Bertani (LB) medium and waste sewage sludge (WSS) under different dilutions and temperatures. When WSS was used as a bacterial source, whereas the highest number of colonies was found at the concentration of WSS (5%), a particular concentration of LB (10%) or WSS (1%) as a growth medium showed the best number of the operational taxonomic units (OTUs) of colonies. The results of bacterial community structure indicated that there are 1, 8, and 12 bacterial genera found uniquely in the agar plates of LB, 10% LB, and 5% WSS. By contrast, when palm oil mill effluent sludge was used as a bacterial source, the effect of dilution was different with WSS. When comparing the biodiversity between colonies and liquid culture, a high OTU value was observed in the colonies on the plate. In addition, 30°C showed the highest number of colonies in LB, 10% LB, and 5% WSS whereas the best OTUs were observed at 37°C for LB and 10% LB, and at 25°C for 5% WSS. This study demonstrates the diversification of cultivable bacteria through the number of OTUs in diluted LB medium and WSS, which is beneficial to isolate a unique bacterial strain.Key points• Impacts of diluted LB medium and WSS for colony formation were determined.• Difference of concentration of LB and WSS made different effects on colony formation.• Temperature change affected on diluted LB and WSS as media.

Highly parallelized droplet cultivation and prioritization of antibiotic producers from natural microbial communities

Antibiotics from few culturable microorganisms have saved millions of lives since the 20th century. But with resistance formation, these compounds become increasingly ineffective, while the majority of microbial and with that chemical compound diversity remains inaccessible for cultivation and exploration. Culturing recalcitrant bacteria is a stochastic process. But conventional methods are limited to low throughput. By increasing (i) throughput and (ii) sensitivity by miniaturization, we innovate microbiological cultivation to comply with biological stochasticity. Here, we introduce a droplet-based microscale cultivation system, which is directly coupled to a high-throughput screening for antimicrobial activity prior to strain isolation. We demonstrate that highly parallelized in-droplet cultivation starting from single cells results in the cultivation of yet uncultured species and a significantly higher bacterial diversity than standard agar plate cultivation. Strains able to inhibit intact reporter strains were isolated from the system. A variety of antimicrobial compounds were detected for a selected potent antibiotic producer.

Metagenomic analysis for profiling of microbial communities and tolerance in metal-polluted pulp and paper industry wastewater

This work aimed to study the profiling and efficiency of microbial communities and their abundance in the pulp and paper industry wastewater, which contained toxic metals, high biological oxygen demands, chemical oxygen demand, and ions contents. Sequence alignment of the 16S rRNA V3-V4 variable region zone with the Illumina MiSeq framework revealed 25356 operating taxonomical units (OTUs) derived from the wastewater sample. The major phyla identified in wastewater were Proteobacteria, Bacteroidetes, Firmicutes, Chloroflexi, Actinobacteria, Spirochetes, Patesibacteria, Acidobacteria, and others including unknown microbes. The study showed the function of microbial communities essential for the oxidation and detoxifying of complex contaminants and design of effective remediation techniques for the re-use of polluted wastewater. Findings demonstrated that the ability of different classes of microbes to adapt and survive in metal-polluted wastewater irrespective of their relative distribution, as well as further attention can be provided to its use in the bioremediation process.

Diversity and plant growth-promoting potential of (un)culturable bacteria in the Hedera helix phylloplane

Background

A diverse community of microbes naturally exists on the phylloplane, the surface of leaves. It is one of the most prevalent microbial habitats on earth and bacteria are the most abundant members, living in communities that are highly dynamic. Today, one of the key challenges for microbiologists is to develop strategies to culture the vast diversity of microorganisms that have been detected in metagenomic surveys.

Results

We isolated bacteria from the phylloplane of Hedera helix (common ivy), a widespread evergreen, using five growth media: Luria–Bertani (LB), LB01, yeast extract–mannitol (YMA), yeast extract–flour (YFlour), and YEx. We also included a comparison with the uncultured phylloplane, which we showed to be dominated by Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. Inter-sample (beta) diversity shifted from LB and LB01 containing the highest amount of resources to YEx, YMA, and YFlour which are more selective. All growth media equally favoured Actinobacteria and Gammaproteobacteria, whereas Bacteroidetes could only be found on LB01, YEx, and YMA. LB and LB01 favoured Firmicutes and YFlour was most selective for Betaproteobacteria. At the genus level, LB favoured the growth of Bacillus and Stenotrophomonas, while YFlour was most selective for Burkholderia and Curtobacterium. The in vitro plant growth promotion (PGP) profile of 200 isolates obtained in this study indicates that previously uncultured bacteria from the phylloplane may have potential applications in phytoremediation and other plant-based biotechnologies.

Conclusions

This study gives first insights into the total bacterial community of the H. helix phylloplane, including an evaluation of its culturability using five different growth media. We further provide a collection of 200 bacterial isolates underrepresented in current databases, including the characterization of PGP profiles. Here we highlight the potential of simple strategies to obtain higher microbial diversity from environmental samples and the use of high-throughput sequencing to guide isolate selection from a variety of growth media.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02119-z.

Revisiting soil bacterial counting methods: Optimal soil storage and pretreatment methods and comparison of culture-dependent and -independent methods

Although a number of different methods have been used to quantify soil bacteria, identifying the optimal method(s) for soil bacterial abundance is still in question. No single method exists for undertaking an absolute microbial count using culture-dependent methods (CDMs) or even culture-independent methods (CIMs). This study investigated soil storage and pretreatment methods for optimal bacterial counts. Appropriate storage temperature (4°C) and optimal pretreatment methods (sonication time for 3 min and centrifugation at 1400 g) were necessary to preserve bacterial cell viability and eliminate interference from soil particles. To better estimate soil bacterial numbers under various cellular state and respiration, this study also evaluated three CDMs (i.e., colony forming unit, spotting, and most probable number (MPN) and three CIMs (i.e., flow cytometry (FCM), epifluorescence microscopy (EM) count, and DNA quantitation). Each counting method was tested using 72 soil samples collected from a local arable farm site at three different depths (i.e., 10-20, 90-100, and 180-190 cm). Among all CDMs, MPN was found to be rapid, simple, and reliable. However, the number of bacteria quantified by MPN was 1-2 orders lower than that quantified by CIMs, likely due to the inability of MPN to count anaerobic bacteria. The DNA quantitation method appeared to overestimate soil bacterial numbers, which may be attributed to DNA from dead bacteria and free DNA in the soil matrix. FCM was found to be ineffective in counting soil bacteria as it was difficult to separate the bacterial cells from the soil particles. Dyes used in FCM stained the bacterial DNA and clay particles. The EM count was deemed a highly effective method as it provided information on soil mineral particles, live bacteria, and dead bacteria; however, it was a time-consuming and labor-intensive process. Combining both types of methods was considered the best approach to acquire better information on the characteristics of indigenous soil microorganisms (aerobic versus anaerobic, live versus dead).