Environmental microbiology最新文献

Selection and dispersal are the primary processes influencing community assembly at both global and regional scales. Although the effectiveness of dispersal is often examined within the same biome, microscopic organisms demonstrate the capability to colonise and thrive across different biomes. In this study, we evaluated the relationship between (i) aquatic, (ii) sedimentary and (iii) aerial microbial communities, and how local selective pressures influence the potential impact of inter-biome dispersal, focusing on the salinity gradient stress over time in ephemeral saline lakes. Our taxonomic ordination analyses revealed that the three communities were distinctly segregated yet interconnected by shared populations. Organisms prevalent across the three biomes exhibited cosmopolitan behaviour based on global databases, indicating an inherent ability to cross biome boundaries. Cosmopolitan groups dominated the planktonic community at lower salinities but gradually diminished as salinity increased, resulting in communities dominated by aquatic specialists with more restricted environmental distributions. The aerial community was primarily composed of generalists, although airborne halophiles were also identified, suggesting long-range dispersal as a source of colonisers in isolated extremophile environments. Our findings contribute to a better understanding of the dynamic interplay between dispersal and selective pressures on community assembly across biomes, highlighting the significance of aerial microbiota in remote colonisation.

The CoA thioester of 2-(carboxymethyl)cyclohexane-1-carboxylic acid has been identified as a metabolite in anaerobic naphthalene degradation by the sulfate-reducing culture N47. This study identified and characterised two acyl-CoA dehydrogenases (ThnO/ThnT) and an intramolecular CoA-transferase (ThnP) encoded within the substrate-induced thn operon, which contains genes for anaerobic degradation of naphthalene. ThnP is a CoA transferase belonging to the family I (Cat 1 subgroup) that catalyses the intramolecular CoA transfer from the carboxyl group of 2-(carboxymethyl)cyclohexane-1-carboxyl-CoA to its carboxymethyl moiety, forming 2-carboxycyclohexylacetyl-CoA. Neither acetyl-CoA nor succinyl-CoA functions as an exogenous CoA donor for this reaction. The flavin-dependent homotetrameric dehydrogenase ThnO is specific for (1R,2R)-2-carboxycyclohexylacetyl-CoA with an apparent K_m value of 61.5 μM, whereas ThnT is a promiscuous enzyme catalysing the same reaction at lower rates. Identifying these three enzymes confirmed the involvement of the thn gene cluster in the anaerobic naphthalene degradation pathway. This study establishes a modified metabolic pathway for anaerobic naphthalene degradation upstream of 2-(carboxymethyl)cyclohexane-1-carboxyl-CoA and provides further insight into the subsequent second-ring cleavage reaction.

Elongated morphologies are prevalent among motile bacterioplankton in aquatic systems. This is often attributed to enhanced chemotactic ability, but how long is best? We hypothesized the existence of an optimal cell length for efficient chemotaxis resulting from shape-imposed physical constraints acting on the trade-off between rapid exploration versus efficient exploitation of nutrient sources. To test this hypothesis, we evaluated the chemotactic performance of elongated cephalexin-treated Escherichia coli towards α-methyl-aspartate in a microfluidic device creating linear, stable and quiescent chemical gradients. Our experiments showed cells of intermediate length aggregating most tightly to the chemoattractant source. A sensitivity analysis of an Individual-Based-Model replicating these results showed that 1) cells of intermediate length are optimal at transient states, whereas at steady state longest cells are best, 2) poor chemotactic performance of very short cells is caused by directionality loss, and 3) long cells are penalized by brief, slow runs. Finally, we evaluated chemotactic performance of cells of different length with simulations of a phycosphere, and found that long cells swimming in a run-and-reverse pattern with extended runs and moderate speeds are most efficient in this microenvironment. Overall, our results suggest that the stability of the chemical landscape plays a role in cell-size selection.

This study investigated the diversity of thermophilic Campylobacter species isolated from three New Zealand freshwater catchments affected by pastoral and urban activities. Utilising matrix-assisted laser desorption ionisation-time of flight and whole genome sequence analysis, the study identified Campylobacter jejuni (n = 46, 46.0%), C. coli (n = 39, 39%), C. lari (n = 4, 4.0%), and two novel Campylobacter species lineages (n = 11, 11%). Core genome sequence analysis provided evidence of prolonged persistence or continuous faecal shedding of closely related strains. The C. jejuni isolates displayed distinct sequence types (STs) associated with human, ruminant, and environmental sources, whereas the C. coli STs included waterborne ST3302 and ST7774. Recombination events affecting loci implicated in human pathogenesis and environmental persistence were observed, particularly in the cdtABC operon (encoding the cytolethal distending toxin) of non-human C. jejuni STs. A low diversity of antimicrobial resistance genes (aadE-Cc in C. coli), with genotype/phenotype concordance for tetracycline resistance (tetO) in three ST177 isolates, was noted. The data suggest the existence of two types of naturalised waterborne Campylobacter: environmentally persistent strains originating from waterbirds and new environmental species not linked to human campylobacteriosis. Identifying and understanding naturalised Campylobacter species is crucial for accurate waterborne public health risk assessments and the effective allocation of resources for water quality management.

The canonical arsRBC genes of the ars1 operon in Pseudomonas putida KT2440, which confer tolerance to arsenate and arsenite, are followed by a series of additional ORFs culminating in phoN1. The phoN1 gene encodes an acetyltransferase that imparts resistance to the glutamine synthetase inhibitor herbicide phosphinothricin (PPT). The co-expression of phoN1 and ars genes in response to environmental arsenic, along with the physiological effects, was analysed through transcriptomics of cells exposed to the oxyanion and phenotypic characterization of P. putida strains deficient in different components of the bifan motif governing arsenic resistance in this bacterium. Genetic separation of arsRBC and phoN1 revealed that their associated phenotypes operate independently, indicating that their natural co-regulation is not functionally required for simultaneous response to the same signal. The data suggest a scenario of associative evolution, akin to Pavlovian conditioning, where two unrelated but frequently co-occurring signals result in one regulating the other's response – even if there is no functional link between the signal and the response. Such surrogate regulatory events may provide an efficient solution to complex regulatory challenges and serve as a genetic patch to address transient gaps in evolving regulatory networks.

Dead fungal cells, known as necromass, are increasingly recognised as significant contributors to long-term soil carbon pools, yet the genes involved in necromass decomposition are poorly understood. In particular, how microorganisms degrade necromass with differing initial cell wall chemical compositions using carbohydrate-active enzymes (CAZymes) has not been well studied. Based on the frequent occurrence and high abundance of the fungal genus Trichoderma on decaying fungal necromass in situ, we grew Trichoderma reesei RUT-C30 on low and high melanin necromass of Hyaloscypha bicolor (Ascomycota) in liquid cultures and assessed T. reesei gene expression relative to each other and relative to glucose. Transcriptome data revealed that T. reesei up-regulated many genes (over 100; necromass versus glucose substrate) coding for CAZymes, including enzymes that would target individual layers of an Ascomycota fungal cell wall. We also observed differential expression of protease- and laccase-encoding genes on high versus low melanin necromass, highlighting a subset of genes (fewer than 15) possibly linked to the deconstruction of melanin, a cell wall constituent that limits necromass decay rates in nature. Collectively, these results advance our understanding of the genomic traits underpinning the rates and fates of carbon turnover in an understudied pool of Earth's belowground carbon, fungal necromass.

Safe geological disposal of radioactive waste requires a thorough understanding of geochemical conditions in the host formation. Boom Clay is a potential candidate in Belgium, where active methanogenesis has been detected in its deep subsurface, influencing the local geochemistry. However, the pathways driving this process and the characteristics of the methanogenic archaea involved remain unclear. We isolated a distinct archaeal strain from Boom Clay pore water and characterized it geno- and phenotypically. Isolate TD41E1-1 belongs to a novel species of the Methanosarcina genus, for which the name Methanosarcina hadiensis sp. nov. is proposed. TD41E1-1 cells are coccus-shaped, irregularly sized cells enveloped by extracellular polymer substances. Growth and substrate utilization experiments and genomic analysis demonstrated that the strain prefers methylated compounds or hydrogen as substrates for methane production. Although it possesses a complete acetoclastic pathway, no growth was observed in the presence of acetate in the tested conditions. Based on its phylogenetic relation to other known Methanosarcina species and on the presence of c-type cytochromes, it can be concluded that the strain likely occupies an intermediate position between type I and type II Methanosarcina species. These findings provide valuable insights for assessing Boom Clay's suitability for geological disposal of radioactive waste.

Bacterivorous nematodes are important grazers in the soil micro-food web. Their trophic regulation shapes the composition and ecosystem services of the soil microbiome, but the underlying population dynamics of bacteria and archaea are poorly understood. We followed soil respiration and 221 dominant bacterial and archaeal 16S rRNA gene amplicon sequencing variants (ASVs) in response to top-down control by a common bacterivorous soil nematode, Acrobeloides buetschlii, bottom-up control by maize litter amendment and their combination over 32 days. Maize litter amendment significantly increased soil respiration, while A. buetschlii addition caused an earlier peak in soil respiration. Underlying bacterial and archaeal population dynamics separated into five major response types, differentiating in their temporal abundance maxima and minima. In-depth analysis of these population dynamics identified a broad imprint of A. buetschlii grazing on dominant bacterial (Acidobacteriota, Bacteroidota, Gemmatimonadota, Pseudomonadota) and archaeal (Nitrososphaerota) ASVs. Combined bottom-up control by maize litter and top-down control by A. buetschlii grazing caused a succession of soil microbiota, driven by population changes first in the Bacteroidota, then in the Pseudomonadota and finally in the Acidobacteriota and Nitrososphaerota. Our results are an essential step forward in understanding trophic modulation of soil microbiota and its feedback on soil respiration.