A major consequence of anthropogenic climate change is the intensification and extension of drought periods. Prolonged drought can alter conditions in drained peatlands and cause disturbances in microbial communities in the topsoil layer of the peat. Varying environmental conditions throughout the growing season, such as the availability of organic matter and nutrients, temperature and water table, further impact these communities and consequently affect carbon and nutrient cycles. The impact of drought and new forestry practices is largely unknown in drained peatland forests. We examined how microbial communities change over a growing season in different harvesting intensities (continuous cover forestry, clear-cut and uncut) in a drained peatland site using bacterial 16S and fungal ITS2 rRNA analysis. We found seasonal differences in bacterial and fungal diversity and species richness, and subtle changes in microbial communities at the phylum and genus levels when comparing various environmental factors. Diversity, species richness and relative abundance differed in spring compared to summer and autumn. However, significant differences in the microbial community structure were not detected. Understanding the responses of microbial communities to disturbances like drought and other environmental factors provides new insights into the consequences of climate change on drained forested peatlands.

Antimicrobial resistance (AMR) is under-monitored in Africa, with few reports characterizing resistant bacteria from the environment. This study examined physicochemical parameters, chemical contaminants and antibiotic-resistant bacteria in waste stabilization pond effluents, hospital wastewater and domestic wastewater from four sewerage sites in Kumasi. The bacteria isolates were sequenced. Three sites exceeded national guidelines for total suspended solids, biochemical oxygen demand, chemical oxygen demand and electrical conductivity. Although sulfamethoxazole levels were low, the antibiotic was detected at all sites. Multi-drug-resistant Klebsiella pneumoniae and Pseudomonas aeruginosa were isolated with multi-locus sequence typing identifying K. pneumoniae strains as ST18 and ST147, and P. aeruginosa as ST235, all of clinical relevance. A comparison of ST147 genomes with isolates from human infections in Africa showed remarkable similarity and shared AMR profiles. Thirteen of the twenty-one plasmids from ST147 harbored at least one AMR gene, including blaCTX-M-15 linked to copper-resistance genes. Our study demonstrated high bacterial counts and organic matter in the analysed wastewater. The recovery of clinically significant isolates with multiple antibiotic and heavy metal resistance genes from the wastewater samples raises public health concerns.

Despite the importance of bacteria in surf zone water quality, detailed insights into their community composition, functions, and seasonal dynamics at recreational beaches are scarce. This study conducted year-long, weekly monitoring of bacterial communities and environmental factors at a recreational beach in Ostend, Belgium. Using full-length 16S rRNA gene sequencing, we correlated bacterial composition and predicted functions with environmental factors to identify potential drivers. Bacterial communities were significantly affected by seasonal variations in chlorophyll a (Chl a), net primary productivity (NPP), and seawater temperature (SWT), with minimal influence from faecal inputs due to human activities. Spring showed distinct abundances of Planktomarina, Amylibacter, and Sulfitobacter, positively correlated with Chl a and related to sulphur oxidation potential. Summer had higher abundances of Cryomorphaceae, likely enhancing chemoheterotrophy. Beginning in mid to late fall and extending into winter, bacterial communities underwent substantial changes. Fall featured a distinctive enrichment of Thioglobaceae, inversely correlated with Chl a. Winter was dominated by Methylophilaceae (OM43 clade), negatively correlated with Chl a, NPP, and SWT. Both seasons exhibited elevated levels of potentially pathogenic phenotypes and predicted functions related to methanol oxidation and methylotrophy. This study provides a baseline for understanding how surf zone bacterial communities respond to environmental changes and impact health.

Corals have complex symbiotic associations that can be influenced by the environment. We compare symbiotic dinoflagellate (family: Symbiodiniaceae) associations and the microbiome of five scleractinian coral species from three different reef habitats in Palau, Micronesia. Although pH and temperature corresponded with specific host-Symbiodiniaceae associations common to the nearshore and offshore habitats, bacterial community dissimilarity analyses indicated minimal influence of these factors on microbial community membership for the corals Coelastrea aspera, Psammocora digitata, and Pachyseris rugosa. However, coral colonies sampled close to human development exhibited greater differences in microbial community diversity compared to the nearshore habitat for the coral species Coelastrea aspera, Montipora foliosa, and Pocillopora acuta, and the offshore habitat for Coelastrea aspera, while also showing less consistency in Symbiodiniaceae associations. These findings indicate the influence that habitat location has on the bacterial and Symbiodiniaceae communities comprising the coral holobiont and provide important considerations for the conservation of coral reef communities, especially for island nations with increasing human populations and development.

Improving our understanding of superficial Streptococcus pyogenes (Strep A) carriage and transmission necessitates robust sampling methods. Here, we compared the effect of storing swab samples in fridge (+4°C) and freezer (-20°C) conditions on the recovery of laboratory-cultured S. pyogenes. Streptococcus pyogenes colony-forming units progressively declined at +4°C, but not at -20°C, over 2 weeks. Results demonstrate that freezing is preferable over refrigeration for storage and transport of skin and throat swabs to ensure that culturing accurately reflects the true results of sampling. This is particularly important in remote community research and practice when immediate incubation is not possible or batch processing is most practical, increasing the elapsed time between collection and laboratory analysis. The study suggests that temperature negatively affects S. pyogenes viability and provides a method to further investigate the role of other environmental factors affecting S. pyogenes transmission.

Vanilla is an economically important crop for low-lying humid tropical regions, but cultivated plants face serious phytosanitary problems. Fusarium wilt is a devastating disease affecting vanilla crops, caused by the fungal pathogens Fusarium oxysporum f. sp. vanillae (Fov) and F. oxysporum f. sp. radicis-vanillae (Forv), part of the F. oxysporum species complex (FOSC). We characterized 29 fungal isolates from a vanilla crop and crop wild relatives (CWR) using molecular (EF1-α and ITS-rRNA loci) and morphological traits. Fusarium was the predominant genus, followed by Colletotrichum and Clonostachys. Four Fusarium species were identified: F. oxysporum (37.9%), Fusarium solani (20.7%), Fusarium pseudocircinatum (13.8%) and Fusarium concentricum (10.3%). The latter three species were isolated only from CWR and may represent latent pathogens. Fov was isolated from both the crop and CWR, while a Forv-affiliated isolate was also found in a vanilla crop, marking the first report in the neotropical region. The EF1-α locus provided greater genotype resolution, as well as having reference sequences for Forv. However, the fungal barcode ITS locus is widely applied. We recommend the continued use of both loci for Fusarium diagnosis in vanilla to facilitate early detection and the development of effective integrated crop management strategies.

Haloarchaea, known for their resilience to environmental fluctuations, require a minimum salt concentration of 10% (w/v) for growth and can survive up to 35% (w/v) salinity. In biotechnology, these halophiles have diverse industrial applications. This study investigates the tolerance responses of nine haloarchaea: Haloferax mediterranei, Haloferax volcanii, Haloferax gibbonsii, Halorubrum californiense, Halorubrum litoreum, Natrinema pellirubrum, Natrinema altunense, Haloterrigena thermotolerans and Haloarcula sinaiiensis, under various stressful conditions. All these archaea demonstrated the ability to thrive in the presence of toxic metals such as chromium, nickel, cobalt and arsenic, and their tolerance to significantly elevated lithium concentrations in the medium was remarkable. Among the studied haloarchaea, Hfx. mediterranei exhibited superior resilience, particularly against lithium, with an impressive minimum inhibitory concentration (MIC) of up to 4 M LiCl, even replacing NaCl entirely. Haloferax species showed specificity for conditions with maximal growth rates, while Htg. thermotolerans and Nnm. altunense displayed high resilience without losing growth throughout the ranges, although these were generally low. ICP-MS results highlighted the impressive intracellular lithium accumulation in Nnm. pellirubrum, emphasizing its potential significance in bioremediation. This research highlights a new characteristic of haloarchaea, their tolerance to high lithium concentrations and the potential for new applications in extreme industrial processes and bioremediation.

To date, little research has been conducted on the landscape-scale distribution of soil microbial communities and the factors driving their community structures in the drylands of Africa. We investigated the influence of landscape-scale variables on microbial community structure and diversity across different ecological zones in Botswana. We used amplicon sequencing of bacterial 16S rRNA gene and fungal internal transcribed spacers (ITS) and a suite of environmental parameters to determine drivers of microbial community structure. Bacterial communities were dominated by Actinomycetota (21.1%), Pseudomonadota (15.9%), and Acidobacteriota (10.9%). The dominant fungal communities were Ascomycota (57.3%) and Basidiomycota (7.5%). Soil pH, mean annual precipitation, total organic carbon, and soil ions (calcium and magnesium) were the major predictors of microbial community diversity and structure. The co-occurrence patterns of bacterial and fungal communities were influenced by soil pH, with network-specific fungi-bacteria interactions observed. Potential keystone taxa were identified for communities in the different networks. Most of these interactions were between microbial families potentially involved in carbon cycling, suggesting functional redundancy in these soils. Our findings highlight the significance of soil pH in determining the landscape-scale structure of microbial communities in Botswana's dryland soils.

Interactions between a host organism and its associated microbiota, including symbiotic bacteria, play a crucial role in host adaptation to changing environmental conditions. Antarctica provides a unique environment for the establishment and maintenance of symbiotic relationships. One of the most extensively studied symbiotic bacteria in invertebrates is Wolbachia pipientis, which is associated with a wide variety of invertebrates. Wolbachia is known for manipulating host reproduction and having obligate or facultative mutualistic relationships with various hosts. However, there is a lack of clear understanding of the prevalence of Wolbachia in terrestrial invertebrates in Antarctica. We present the outcomes of a literature search for information on the occurrence of Wolbachia in each of the major taxonomic groups of terrestrial invertebrates (Acari, Collembola, Diptera, Rotifera, Nematoda, Tardigrada). We also performed profiling of prokaryotes based on three marker genes and Kraken2 in available whole genome sequence data obtained from Antarctic invertebrate samples. We found no reports or molecular evidence of Wolbachia in these invertebrate groups in Antarctica. We discuss possible reasons underlying this apparent absence and suggest opportunities for more targeted future research to confirm bacteria's presence or absence.

Lingonberries (Vaccinium vitis-idaea L.), rowanberries (Sorbus aucuparia L.) and rosehips (Rosa canina L.) positively affect human health due to their healing properties, determined by a high content of bioactive compounds. The consumption of unprocessed wild berries is relevant and encouraged, making their in-depth microbiological characterization essential for food safety. This study presents the first high-throughput sequencing analysis of bacterial and fungal communities distributed on the surface of lingonberries, rowanberries and rosehips. Significant plant-defined differences in the taxonomic composition of prokaryotic and eukaryotic microbiota were observed. The bacterial community on rosehips was shown to be prevalent by Enterobacteriaceae, lingonberries by Methylobacteriaceae and rowanberries by Sphingomonadaceae representatives. Among the fungal microbiota, Dothioraceae dominated on rosehips and Exobasidiaceae on lingonberries; meanwhile, rowanberries were inhabited by a similar level of a broad spectrum of fungal families. Cultivable yeast profiling revealed that lingonberries were distinguished by the lowest amount and most distinct yeast populations. Potentially pathogenic to humans or plants, as well as beneficial and relevant biocontrol microorganisms, were identified on tested berries. The combination of metagenomics and a cultivation-based approach highlighted the wild berries-associated microbial communities and contributed to uncovering their potential in plant health, food and human safety.

Heavy metal pollution, particularly cadmium, poses severe environmental and health risks due to its high toxicity and mobility, necessitating effective remediation strategies. While both microbially induced carbonate precipitation (MICP) and humic acid adsorption are promising methods for heavy metal mitigation, their combined effects, particularly the influence of humic acid on the MICP process, have not been thoroughly investigated. This study explores the interaction between humic acid and MICP, revealing that humic acid significantly inhibits the MICP process by reducing urease activity, with the 10% humic acid treatment resulting in a 23.8% reduction in urease activity compared to the control. Additionally, while higher concentrations of humic acid did not significantly reduce cadmium ion concentrations, they did result in a slight increase in organically bound cadmium, indicating an interaction that could alter metal speciation in the soil. These findings provide important insights into the mechanisms by which humic acid affects MICP, offering a foundation for optimizing combined remediation approaches. Future research should aim to fine-tune the balance between MICP and humic acid to enhance the overall efficiency of cadmium remediation strategies. This study contributes to the development of more effective and sustainable methods for addressing cadmium contamination.

Black fungi on rock surfaces endure a spectrum of abiotic stresses, including UV radiation. Their ability to tolerate extreme conditions is attributed to the convergent evolution of adaptive traits, primarily highly melanized cell walls. However, studies on fungal melanins have not provided univocal results on their photoprotective functions. Here, we investigated whether the black fungi Knufia petricola and Cryomyces antarcticus only use DHN melanin or may employ alternative mechanisms to counteract UV-induced damage. For this, melanized wild types and non-melanized Δpks1 mutants were exposed to different doses of UV-B (312 nm) followed by incubation in constant darkness or in light-dark cycles to allow light-dependent DNA repair by photolyases (photoreactivation). C. antarcticus could tolerate higher UV-B doses but was sensitive to white light, whereas K. petricola showed the opposite trend. DHN melanin provided UV-B protection in C. antarcticus, whereas the same pigment or even carotenoids proved ineffective in K. petricola. Both fungi demonstrated functional photoreactivation in agreement with the presence of photolyase-encoding genes. Our findings reveal that although the adaptive trait of DHN melanization commonly occurs across black fungi, it is not equally functional and that there are species-specific adaptations towards either UV-induced lesion avoidance or repair strategies.

Given the threat to public health posed by antibiotic resistance transmission, environmental monitoring is essential for tracking antibiotic resistance genes (ARGs). Houseflies, being ubiquitous organisms capable of carrying and disseminating ARGs, serve as suitable indicators for environmental monitoring. In this study, we employ metagenomic approaches to investigate housefly body surface samples from five typical sites associated with human activities. The investigation reveals microbiome diversity among the samples, along with variations in the occurrence and mobility potential of ARGs. Metagenomic analysis indicates that the composition of ARGs on housefly body surfaces is influenced by environmental ARGs, which may be enriched on the housefly body surface. The resistance genes related to multidrug, β-lactam, bacitracin, and tetracycline were the predominant ARGs detected, with multidrug-related ARGs consistently exhibiting dominance. Furthermore, the abundance of ARGs in the different housefly body surface samples was found to correlate with the population density and mobility of the sampling site. Natural environments exhibited the lowest ARG abundance, while areas with higher population density and limited population mobility displayed higher ARG abundance. This study emphasizes the effectiveness of houseflies as monitors for environmental ARGs and underscores their potential for assessing and controlling antibiotic resistance risks in urban environments.

Cost of bacteriophage resistance (COR) is important in explaining processes of diversification and coexistence in microbial communities. COR can be expressed in different traits, and the lack of universally applicable methods to measure fitness trade-offs makes COR challenging to study. Due to its fundamental role in growth, we explored protein synthesis as a target for quantifying COR. In this study, the growth kinetics of three genome-sequenced strains of phage-resistant Escherichia coli, along with the phage-susceptible wild-type, were characterized over a range of glucose concentrations. Bioorthogonal non-canonical amino acid tagging (BONCAT) was used to track differences in protein synthetic activity between the wild-type and phage-resistant E. coli. Two of the resistant strains, with different levels of phage susceptibility, showed mucoid phenotypes corresponding with mutations in genes associated with the Rcs phosphorelay. These mucoid isolates, however, had reduced growth rates and potentially lower protein synthetic activity. Another resistant isolate with a different mutational profile maintained the same growth rate as the wild-type and showed increased BONCAT fluorescence, but its yield was lower. Together, these findings present different patterns of trade-offs resulting from the phage-induced mutations and demonstrate the potential applicability of BONCAT as a tool for measuring COR.

Bioremediation of degraded soils is increasingly necessary due to rising food demand, reductions in agricultural productivity, and limitations in total available arable area. Several bioremediation strategies could be utilized to combat soil degradation, with phytoremediation emerging as a standout option due to its in situ approach and low implementation and maintenance costs compared to other methods. Phytoremediation is also a sustainable solution, which is increasingly desirable to blunt the progression of global warming. Actinorhizal plants display several desirable traits for application in phytoremediation, including the ability to revegetate saline soil and sequester heavy metals with low foliar translocation. Additionally, when grown in association with Frankiaceae endophytes, these abilities are improved and expanded to include the degradation of anthropogenic pollutants and the restoration of soil fertility. However, despite this significant potential to remediate marginalized land, the actinorhizal-Frankiaceae symbiosis remains heavily understudied and underutilized. This review aims to collate the scattered studies that demonstrate these bioremediation abilities and explain the mechanics behind such abilities to provide the necessary insight. Finally, this review will conclude with proposed future directions for utilizing this symbiosis and how it can be optimized further to facilitate improved bioremediation outcomes.

Wheat (Triticum sp.) is a staple cereal crop, providing nearly a fifth of the world's protein and available calories. While fungi associated with wheat plants have been known for centuries, attention to fungi associated with wheat seeds has increased over the last hundred years. Initially, research focused on fungal taxa that cause seed-borne diseases. Seeds act as a physical link between generations and host specialized fungal communities that affect seed dormancy, germination, quality, and disease susceptibility. Interest in beneficial, non-disease-causing fungal taxa associated with seeds has grown since the discovery of Epichloë in fescue, leading to a search for beneficial fungal endophytes in cereal grains. Recent studies of the wheat seed mycobiome have shown that disease, seed development, and temporal variation significantly influence the composition and structure of these fungal communities. This research, primarily descriptive, aims to better understand the wheat seed mycobiome's function in relation to the plant host. A deeper understanding of the wheat seed mycobiome's functionality may offer potential for microbiome-assisted breeding.

Antibiotic resistance genes (ARGs) are ancient and widespread in natural habitats, providing survival advantages for microbiomes under challenging conditions. In mountain ecosystems, phyllosphere bacterial communities face multiple stress conditions, and the elevational gradients of mountains represent crucial environmental gradients for studying biodiversity distribution patterns. However, the distribution patterns of ARGs in the phyllosphere along elevational gradients, and their correlation with bacterial community structures, remain poorly understood. Here, we applied metagenomic analyses to investigate the abundance and diversity of ARGs in 88 phyllosphere samples collected from Mount Tianmu, a national natural reserve. Our results showed that the abundance of ARGs in the phyllosphere increased along elevational gradients and was dominated by multidrug resistance and efflux pumps. The composition of bacterial communities, rather than plant traits or abiotic factors, significantly affected ARG abundance. Moreover, increased ARG abundance was correlated with greater phylogenetic overdispersion and a greater proportion of negative associations in the bacterial co-occurrence networks, suggesting that bacterial competition primarily shapes phyllosphere resistomes. These findings constitute a major advance in the biodiversity of phyllosphere resistomes along elevations, emphasizing the significant impact of bacterial community structure and assembly on ARG distribution, and are essential for understanding the emergence of ARGs.

Dish sponges are known to support the proliferation of human bacterial pathogens, yet they are commonly used by consumers. Exposure to foodborne pathogens via sponge use may lead to illness, a serious concern among susceptible populations. The extent of exposure risks from sponge use has been limited by constraints associated with culture-independent or dependent methods for bacterial community characterization. Therefore, five used dish sponges were characterized to evaluate the presence of viable bacterial foodborne pathogens using the novel application of propidium monoazide (PMA) treatment and targeted 16S rRNA gene amplicon sequencing. Select pathogen viability was confirmed using targeted selective enrichment. The taxonomic abundance profiles of total and viable sponge microbiomes did not vary significantly. The numbers of unique bacterial species (p = 0.0465) and foodborne pathogens (p = 0.0102) identified were significantly lower in viable sponge microbiomes. Twenty unique bacterial foodborne pathogens were detected across total and viable sponge microbiomes, and three to six viable foodborne pathogens were identified in each sponge. Escherichia coli and Staphylococcus aureus were identified in each viable sponge microbiome, and viable E. coli were recovered from two sponges via targeted selective enrichment. These findings suggest that sponge-associated bacterial communities are primarily viable and contain multiple viable bacterial foodborne pathogens.

Marine animals often harbour complex microbial communities that influence their physiology. However, strong evidence for resident microbiomes in marine bivalves is lacking, despite their contribution to estuarine habitats and coastal economies. We investigated whether marine bivalves harbour stable, resident microorganisms in specific tissues or if their microbiomes primarily consist of transient members reflecting the environmental microbial pool. Conducting a latitudinal study of wild eastern oysters (Crassostrea virginica) along the East Coast of the United States, we aimed to identify resident microorganisms that persist across a wide geographical range. Our results revealed that microbial communities in seawater and sediment samples followed latitudinal diversity patterns driven by geographic location. In contrast, oyster-associated microbiomes were distinct from their surrounding environments and exhibited tissue-specific compositions. Notably, oyster microbiomes showed greater similarity within the same tissue type across different geographic locations than among different tissue types within the same location. This indicates the presence of tissue-specific resident microbes that persist across large geographical ranges. We identified a persistent set of resident microbiome members for each tissue type, with key microbial members consistent across all locations. These findings underscore the oyster host's role in selecting its microbiome and highlight the importance of tissue-specific microbial communities in understanding bivalve-associated microbiomes.

We aimed to evaluate the ability of naturally occurring colonies of Microcystis, embedded in a thick mucilage, to persist in estuarine waters. In two batch experiments, we examined the dynamics of microbial communities, including cyanobacteria and associated heterotrophic bacteria, sampled from the field during both a cyanobacterial bloom (non-limiting nutrient condition) and the post-bloom period (limiting nutrient condition), and subjected them to a salinity gradient representative of the freshwater-marine continuum. We demonstrated that both Microcystis aeruginosa and M. wesenbergii survived high salinities due to osmolyte accumulation. Specifically, prolonged exposure to high salinity led to betaine accumulation in the cyanobacterial biomass. The relative abundance of the mcyB gene remained around 30%, suggesting no selection for toxic genotypes with salinity or nutrient changes. Microcystins were predominantly intracellular, except at high salinity levels (>15), where more than 50% of the total microcystin concentration was extracellular. In both nutrient conditions, over 70% of the heterotrophic bacterial community belonged to the Gammaproteobacteria family, followed by the Bacteroidota. Bacterial community composition differed in both size fractions, as well as along the salinity gradient over time. Finally, genus-specific core microbiomes were identified and conserved even under highly stressful conditions, suggesting interactions that support community stability and resilience.

Antimicrobial resistance (AMR), known as the "silent pandemic," is exacerbated by pathogenic bacteria's ability to form biofilms. Marine compounds hold promise for novel antibacterial drug discovery. Two isolates from preliminary saltwater environment screening demonstrated antimicrobial activity and were subsequently identified as Bacillus subtilis MTUA2 and Bacillus velezensis MTUC2. Minimum inhibitory concentrations (MICs), minimum biofilm inhibition concentrations (MBICs) and minimum biofilm eradication concentrations (MBECs) required to prevent and/or disrupt bacterial growth and biofilm formation were established for MRSA, Staphylococcus aureus, Acinetobacter baumannii and Escherichia coli. The metabolic activity within biofilms was determined by the 2,3,5-triphenyltetrazolium chloride assay. Both Bacillus species exhibited unique antimicrobial effects, reducing MRSA and S. aureus planktonic cell growth by 50% and sessile cell growth for S. aureus and E. coli by 50% and 90%, respectively. No effect was observed against A. baumannii. Significant MBIC and MBEC values were achieved, with 99% inhibition and 90% reduction in MRSA and S. aureus biofilms. Additionally, 90% and 50% inhibition was observed in E. coli and A. baumannii biofilms, respectively, with a 50% reduction in E. coli biofilm. These findings suggest that the mode of action employed by B. subtilis MTUA2 and B. velezensis MTUC2 metabolites should be further characterized and could be beneficial if used independently or in combination with other treatments.