Search Results (34)

Microorganisms represent the Earth’s most abundant biomass and a vast reservoir of genetic diversity. However, traditional agar plate methods fail to recover the vast majority of these species, leaving a “microbial dark matter” that holds immense potential for the discovery of novel antibiotics and bioactive compounds. While conventional techniques such as selective media and enrichment culture remain foundational, they are inherently limited by community biases and the inability to support low-abundance, oligotrophic species. To address these bottlenecks, a diverse array of innovative isolation strategies has emerged. This review systematically categorizes and evaluates these methodologies, ranging from in situ cultivation to high-resolution single-cell manipulation. We first examine membrane diffusion-based cultivation (e.g., iChip), which mimics natural microenvironments to resuscitate recalcitrant microbes. Subsequently, we explore high-throughput single-cell technologies, including microfluidics for physicochemical separation, optical tweezers for precise manipulation, and fluorescence-activated cell sorting (FACS). Special attention is given to Raman-activated cell sorting (RACS) as a label-free functional screening tool and reverse genomics for targeted capture. By synthesizing the strengths and limitations of these approaches, we propose integrated workflows designed to accelerate the mining of untapped microbial resources. Full article

Artificial cyanobacterial crusts (ACCs) are a potentially effective biological strategy for combating desertification. However, while functional microorganisms influence ACCs formation efficiency, research on their role is limited, and their underlying promotion mechanisms remain unclear. Here, we investigated the effects of three functional synthetic microbial communities (SynComs), each dominated by microorganisms specialized in exopolysaccharide (EPS) production (3 strains), siderophore production (3 strains), or nitrogen fixation (4 strains), on ACCs formation following inoculation with Microcoleus vaginatus. This study was carried out in a controlled laboratory setting with a 12 h light/dark cycle and a light intensity of 2400–2700 lux. Following a 24-day cultivation period, EPS-producing or nitrogen-fixing SynComs significantly increased the chlorophyll-a content by 16.0–16.3%. Except for the nitrogen-fixing bacteria treatment, other SynComs enhanced the soil organic matter content of ACCs by 9.1% to 27.3%. The content of EPS was significantly improved by all three SynComs by 14.1~19.2%. Urease activity rose by 6.7% when siderophore-producing bacteria were added. The impacts of SynComs on ammonium nitrogen (NH₄⁺-N) showed different temporal dynamics: nitrogen-fixing SynComs significantly increased NH₄⁺-N early (≤10 days), while EPS-producing and siderophore-producing SynComs enhanced accumulation later (17–24 days). SynComs inoculation markedly accelerated cyanobacterial and general microbial colonization and growth. In comparison to day 0, the 16S rRNA gene copy number of ACCs increased by 24.1% and 43.0%, respectively, in the EPS-producing and nitrogen-fixing SynComs. Additionally, correlation analysis showed that SynComs transformed the weak correlations in the control into a strong positive correlation between NH₄⁺-N and both Chl-a and microbial biomass. Our findings demonstrate SynComs, particularly the EPS-producing or nitrogen-fixing SynComs, enhance ACCs formation through elucidated mechanisms, providing a theoretical basis for optimizing ACCs-based desertification control strategies. Full article

The vast majority of microorganisms in the environment remain uncultured using conventional laboratory techniques, representing an immense untapped reservoir of genetic and chemical diversity. Recent innovations in cultivation strategies, combined with advances in metagenomics, single-cell genomics, and synthetic biology, have opened new avenues for accessing and harnessing bioactive natural products from these previously inaccessible microorganisms. This review highlights recent methodological and technological advancements in the cultivation and identification of novel microorganisms, and showcases the resulting discoveries of new natural products, demonstrating their potential for drug development. Full article

The symbiotic microbiome constitutes a consortium that has been persistently domesticated by a specific algal species, fostering a close and enduring association with the host. The majority of microbial taxa remain uncharacterized. These unknown microbes, often referred to as “microbial dark matter (MDM)”, have important ecological contributions. Given the challenges in discerning symbiotic microbes in natural environments, herein, ecological characteristics of MDM and known taxa within symbiotic communities were investigated in a simulated bloom process using Alexandrium pacificum without antibiotic treatment. Specifically, increased diversification was observed in MDM along the bloom process. Higher trophic interaction and less vulnerability of the molecular network were found in MDM taxa. The “bridge” role of MDM species was better than that of known taxa, as shown by higher betweenness centralization. Deterministic processes dominated in MDM taxa, which promote phylogenic diversity of such groups to some extent. The findings highlight that MDM taxa play an important role in sustaining community stability and functioning. This study broadens our understanding of the ecological contribution of MDM under disturbances from dinoflagellate blooms, providing essential theoretical insights and empirical data to inform the management of coastal toxic blooms. Full article

This study aimed to investigate vertical variations in dissolved organic matter (DOM) properties, humus (HS) composition, humic acid (HA) characteristics, and clay mineral dynamics, with a particular focus on the vertical distribution of HS components and mineral composition across Dark-brown, Meadow, and Paddy soil profiles. Results indicated that: (1) DOM in all three soil types was predominantly endogenous, primarily derived from microbial metabolism with minimal contributions from plant residues. (2) Vertical trends in DOM carbon content (C_DOM) were specific to soil type: in Dark-brown soil, C_DOM slightly increased from the Ap to Bt layer, followed by a sharp increase in the C layer; Meadow soil exhibited a significant decrease in C_DOM in the AB layer but remained relatively stable in other layers; Paddy soil showed a consistent decline in C_DOM with increasing depth. (3) HS and its fractions exhibited vertical variability: Paddy soil showed higher HS content in surface layers; carbon contents of water-soluble substances, HA, and humic-extracted acid (C_WSS, C_HA, and C_HE) decreased with depth in Dark-brown and Paddy soils, whereas they remained relatively stable in deeper layers of Meadow soil. (4) HA characteristics, including C/N ratio, functional groups, and aromaticity, were influenced by both depth and soil type: the Ap2 layer of Paddy soil effectively restricted the downward movement of organic matter; Fe³⁺ complexation played a key role in HA stabilization in Dark-brown soil; Meadow soil exhibited transitional HS properties. (5) Clay mineral assemblages were dominated by 2:1 type minerals (illite, smectite, illite–smectite interstratifications), showing distinct vertical weathering patterns: illite content decreased with depth due to hydrolysis, while proton-driven dissolution promoted kaolinite formation in surface layers, particularly in Dark-brown soil 2:1 minerals enhancing organic–mineral complexation in Meadow soil. The findings of this study provided a scientific basis for optimizing soil carbon pool management and offer insights into organic–mineral interactions that can enhance organic matter sequestration in agricultural soils. Full article

Olive oil production generates vast quantities of by-products, with olive mill wastewater (OMW) being a particularly challenging effluent. Characterized by its dark color, high acidity, and rich composition of organic matter, phenolic compounds, and residual oils, OMW resists conventional degradation methods and poses significant environmental risks due to its phytotoxicity and microbial inhibition. Addressing this issue requires sustainable solutions that align with circular economy principles. A promising strategy involves the biotechnological valorization of OMW using the non-conventional yeast Yarrowia lipolytica, which thrives on organic-rich substrates and converts them into high-value metabolites. This review provides a comprehensive analysis of recent advances in Y. lipolytica applications for OMW valorization, emphasizing its role in developing eco-friendly industrial processes. It begins by outlining the physicochemical challenges of OMW and the metabolic versatility of Y. lipolytica, including its ability to adapt to acidic, phenolic-rich environments. Subsequent sections critically evaluate the yeast’s capacity to synthesize commercially valuable products such as lipases (used in the food and biofuel industries), citric acid (a food and pharmaceutical additive), and polyols like mannitol and erythritol (low-calorie sweeteners). Strategies to optimize microbial productivity, such as substrate pre-treatment, nutrient supplementation, and process engineering, are also discussed. By synthesizing current research, the review highlights how Y. lipolytica-driven OMW valorization can mitigate environmental harm while creating economic opportunities, bridging the gap between waste management and green chemistry. Full article

Groundwater harbors phylogenetically diverse Candidate Phyla Radiation (CPR) bacteria, representing an ideal ecosystem for studying this microbial dark matter. However, no CPR strains have been successfully isolated from groundwater, severely limiting further research. This study employed a multi-metagenome approach, integrating time-resolved sampling, antibiotic/nutrient interventions, and microbial correlation networks to unravel CPR ecological roles in groundwater and provide insights into their subsequent cultivation. Through 36 metagenomes from a groundwater system containing at least 68 CPR phyla, we revealed the time-sensitive collapse of CPR communities: total abundance plummeted from 7.9% to 0.15% within 48 h post-sampling, driven by competition with rapidly dividing non-CPR bacteria, such as members of Pseudomonadota. Ampicillin (100 mg/L) stabilized CPR communities by suppressing competitors, whereas low-nutrient conditions paradoxically reversed this effect. Long-term enrichment (14 months) recovered 63 CPR phyla (0.35% abundance), revealing their survival resilience despite nutrient deprivation. Correlation networks prioritized Actinomyces, a novel Acidimicrobiaceae genus, Aestuariivirga, Baekduia and Caedimonadaceae as potential CPR partners, providing actionable targets for co-culture trials. Here, we propose actionable recommendations spanning groundwater sampling, activation status, identification of CPR symbiotic partners, and optimization of culture conditions, which bypass traditional blind cultivation and are critical for future efforts to cultivate CPR bacterial strains from groundwater. Cultivating CPR bacteria will contribute to clarifying their diversity, ecological roles, evolutionary mechanisms, metabolic pathways, and genetic potential. Full article

Composting is an environmentally friendly treatment technology that recycles and sanitizes organic solid waste. This study aimed to assess the evolution of nutrients, maturity, and microbial communities during the composting of different plant-derived wastes. The composting process was conducted over 49 days using three types of plant-derived waste: wheat bran (WB), peanut straw (PS), and poplar leaf litter (PL). This process was examined through physical, chemical, and biological parameters. The results revealed that after 49 days of composting, the three groups experienced significant changes. They were odorless, were insect-free, exhibited a dark brown color, had an alkaline pH value, and had an electrical conductivity (EC) value of less than 4 mS/cm. These characteristics indicated that they had reached maturity. Nutrient content was the most significant factor influencing the degree of humification of the different composting materials, while changes in microbial community diversity were the key driving factors. Significantly, the compost PS, derived from peanut straw, entered the thermophilic phase first, and by the end of composting, it had the lowest organic matter (OM) loss rate (17.4%), with increases in total nitrogen (TN), total phosphorus (TP), and total potassium (TK) in the order of PS > PL > WB. The increase in humus carbon (HSC) content and the humic acid/fulvic acid (HA/FA) ratio followed the order PS > WB > PL. FTIR spectra indicated that PS had greater aromatic characteristics compared to the other samples. The abundance and diversity of bacterial and fungal communities in the compost increased significantly, accompanied by more complex community structures. Crucially, there were no phytotoxic effects in any of the three composting treatments, and the compost PS boasted a high germination index (GI) of 94.79%, with the lowest heavy metal contents. The findings indicate that the compost PS has the highest potential for resource utilization and is suitable for agricultural applications. Our results demonstrate that composting technology for plant-derived waste has the potential to enhance soil fertility and provide a reference for the composting treatment and resource utilization of other plant-derived waste. Full article

The domain of Archaea has gathered significant interest for its ecological and biotechnological potential and its role in helping us to understand the evolutionary history of Eukaryotes. In comparison to the bacterial domain, the number of adequately described members in Archaea is relatively low, with less than 1000 species described. It is not clear whether this is solely due to the cultivation difficulty of its members or, indeed, the domain is characterized by evolutionary constraints that keep the number of species relatively low. Based on molecular evidence that bypasses the difficulties of formal cultivation and characterization, several novel clades have been proposed, enabling insights into their metabolism and physiology. Given the extent of global sampling and sequencing efforts, it is now possible and meaningful to question the magnitude of global archaeal diversity based on molecular evidence. To do so, we extracted all sequences classified as Archaea from 500 thousand amplicon samples available in public repositories. After processing through our highly conservative pipeline, we named this comprehensive resource the ‘Global Archaea Diversity’ (GAD), which encompassed nearly 3 million molecular species clusters at 97% similarity, and organized it into over 500 thousand genera and nearly 100 thousand families. Saline environments have contributed the most to the novel taxa of this previously unseen diversity. The majority of those 16S rRNA gene sequence fragments were verified by matches in metagenomic datasets from IMG/M. These findings reveal a vast and previously overlooked diversity within the Archaea, offering insights into their ecological roles and evolutionary importance while establishing a foundation for the future study and characterization of this intriguing domain of life. Full article

The vertical distribution patterns of daily primary production and dark carbon fixation were investigated at three stations in the East/Japan Sea (hereafter East Sea), a semi-enclosed marginal sea in the northwest Pacific Ocean. Our results displayed consistent vertical patterns of daily primary production at two of the stations, while the third station exhibited a markedly different distribution pattern, highlighting localized variations in production dynamics. In contrast, dark carbon fixations displaying varying vertical patterns among the stations are not specific enough to have much meaning. Water column-integral values showed differences in the contribution of dark carbon fixation to total primary production, ranging from 4.5% to 27.1%. These variations may reflect environmental parameters such as nutrient concentrations. However, our study is limited by the lack of direct data on the microbial community structure and chemoautotrophic activities, which are crucial for a more comprehensive understanding of these patterns. Understanding the environmental drivers of dark carbon fixation is crucial for elucidating carbon cycling dynamics in the East Sea. Notably, dark carbon fixation could contribute up to one-third of primary production in the region as an additional source of newly produced organic matter, highlighting the need for further investigation into this previously overlooked process. Full article

The applicability of ionic liquids has grown exponentially over the last few decades. This growth is due to the easy modification of these compounds formed by ions, through the proper choice of both moieties, and the possibility of introducing functional groups into their cations and anions. However, studies of their toxicity and effects on the environment remain scarce. This study analyses firstly the response to adding different concentrations of choline dihydrogen phosphate to the germination of seeds of eight plant species. It also examines the microbial population and the respiration of two soils with contrasting organic matter contents. Seeds were incubated in a Petri dish in a Phytotron with a photoperiod of 16 h under light at 24 °C and 8 h in darkness at 16 °C. The activity of microbial populations of untreated and treated soils was analysed by isothermal microcalorimetry at 25 °C. Basal soil respiration kinetics were measured at optimal moisture (80% of field water retention capacity) and temperature (25 °C) over 10 days. The results indicate that this compound has diverse effects on the different endpoints. Nevertheless, this compound can be classified as non-toxic considering its effects on seeds and on soil, at least in the medium- to long-term. Full article

Large quantities of cover crop residues in the soil, combined, or not, with the inoculation of seeds with diazotrophic bacteria, can increase organic matter (OM) and protect soil microorganisms, such as arbuscular mycorrhizal fungi (AMF) and dark septate endophytic (DSE) fungi. Thus, the use of these sustainable biotechnologies can benefit microbial interactions, soil fertility and rice production in the Brazilian Cerrado region. In this study, we evaluated the effects of maize and Urochloa ruziziensis, intercropped or individually, as cover crops and an inoculation of Azospirillum brasilense on the chemical (fertility) and biological (C–microbial biomass and C–CO₂ released) attributes of soil and the effects of root colonization by AMF and DSE on the yield of rice grown in succession in highlands. The experiment was conducted under field conditions, in a typical dystrophic Red Oxisol. The experimental design consisted of randomized blocks arranged in strips, incorporating a combination of eight residual cover crops: ((1) maize, (2) maize–I (I = inoculation of seeds with A. brasilense), (3) Urochloa (U. ruziziensis), (4) Urochloa–I, (5) maize + Urochloa–I, (6) maize + Urochloa–I, (7) maize–I + Urochloa and (8) maize–I + Urochloa–I). This was accompanied by two treatments of rice as a successor crop (inoculated or not with A. brasilense), with four replicates, totaling 64 experimental units. A cover crop and rice seed inoculation prompted increases in OM and AMF relative to DSE, while the inoculation of rice, regardless of the cover crop treatment, increased the soil’s P content. The combination of maize + Urochloa–I and inoculated rice as the next crop generated increases in its sum of bases (SBs) and cation exchange capacity (CEC). There was a 19% increase in rice grain yields when the seed was inoculated. Full article

Gnotobiotic murine models are important to understand microbiota–host interactions. Despite the role of bacteriophages as drivers for microbiome structure and function, there is no information about the structure and function of the gut virome in gnotobiotic models and the link between bacterial and bacteriophage/prophage diversity. We studied the virome of gnotobiotic murine Oligo-MM12 (12 bacterial species) and reduced Altered Schaedler Flora (ASF, three bacterial species). As reference, the virome of Specific Pathogen-Free (SPF) mice was investigated. A metagenomic approach was used to assess prophages and bacteriophages in the guts of 6-week-old female mice. We identified a positive correlation between bacteria diversity, and bacteriophages and prophages. Caudoviricetes (82.4%) were the most prominent class of phages in all samples with differing relative abundance. However, the host specificity of bacteriophages belonging to class Caudoviricetes differed depending on model bacterial diversity. We further studied the role of bacteriophages in horizontal gene transfer and microbial adaptation to the host’s environment. Analysis of mobile genetic elements showed the contribution of bacteriophages to the adaptation of bacterial amino acid metabolism. Overall, our results implicate virome “dark matter” and interactions with the host system as factors for microbial community structure and function which determine host health. Taking the importance of the virome in the microbiome diversity and horizontal gene transfer, reductions in the virome might be an important factor driving losses of microbial biodiversity and the subsequent dysbiosis of the gut microbiome. Full article

The phylum Chloroflexota (formerly Chloroflexi) encompasses metabolically diverse bacteria that often have high prevalence in terrestrial and aquatic habitats, some even with biotechnological application. However, there is substantial disagreement in public databases which lineage should be considered a member of the phylum and at what taxonomic level. Here, we addressed these issues through extensive phylogenomic analyses. The analyses were based on a collection of >5000 Chloroflexota genomes and metagenome-assembled genomes (MAGs) from public databases, novel environmental sites, as well as newly generated MAGs from publicly available sequence reads via an improved binning approach incorporating covariance information. Based on calculated relative evolutionary divergence, we propose that Candidatus Dormibacterota should be listed as a class (i.e., Ca. Dormibacteria) within Chloroflexota together with the classes Anaerolineae, Chloroflexia, Dehalococcoidia, Ktedonobacteria, Ca. Limnocylindria, Thermomicrobia, and two other classes containing only uncultured members. All other Chloroflexota lineages previously listed at the class rank appear to be rather orders or families in the Anaerolineae and Dehalococcoidia, which contain the vast majority of genomes and exhibited the strongest phylogenetic radiation within the phylum. Furthermore, the study suggests that a common ecophysiological capability of members of the phylum is to successfully cope with low energy fluxes. Full article

The order Saprospirales, a group of bacteria involved in complex degradation pathways, comprises three officially described families: Saprospiraceae, Lewinellaceae, and Haliscomenobacteraceae. These collectively contain 17 genera and 31 species. The current knowledge on Saprospirales diversity is the product of traditional isolation methods, with the inherited limitations of culture-based approaches. This study utilized the extensive information available in public sequence repositories combined with recent analytical tools to evaluate the global evidence-based diversity of the Saprospirales order. Our analysis resulted in 1183 novel molecular families, 15,033 novel molecular genera, and 188 K novel molecular species. Of those, 7 novel families, 464 novel genera, and 1565 species appeared in abundances at ≥0.1%. Saprospirales were detected in various environments, such as saline water, freshwater, soil, various hosts, wastewater treatment plants, and other bioreactors. Overall, saline water was the environment showing the highest prevalence of Saprospirales, with bioreactors and wastewater treatment plants being the environments where they occurred with the highest abundance. Lewinellaceae was the family containing the majority of the most prevalent species detected, while Saprospiraceae was the family with the majority of the most abundant species found. This analysis should prime researchers to further explore, in a more targeted way, the Saprospirales proportion of microbial dark matter. Full article