Environmental Microbiology Reports最新文献

Little is known about virome changes in raw and drinking water over time, and differences between raw water sources and treatment technologies. This study used metagenomics to assess viruses prevalent in raw and drinking water samples over 1 year from six Swedish drinking water treatment plants (DWTPs) with varying treatment barriers and with different raw water sources. Sequences homologous to known viruses in the raw water samples were detected by amplification and next-generation sequencing and classified into 152 different virus species belonging to 76 virus families/orders. The majority were small bacteriophages. Other viral genomes were homologous to viruses infecting plants, invertebrates, vertebrates, mammals and giant viruses infecting amoeba or algae. Several virus species were simultaneously found in both raw and drinking water, indicating passage through the purification barriers, although reduced by 1–3 log₁₀ after treatment. Most viruses detected in water samples after ultrafiltration were small viruses, and other barriers appeared more effective at removing smaller viruses. To avoid detecting viruses possibly replicating within DWTPs, viruses were separated according to the possibility that the host could be found in the water sources or not. These results underscore the importance of monitoring both raw and drinking water for small viruses, especially when viral contamination of the source water is at risk, to ensure drinking water quality.

Anthropization of Palaeolithic caves may cause cave microbiota dysbiosis and promote the development of microbial stains on cave walls. In certain cases, chemical biocides have been used to mitigate rock alterations, but this may exacerbate microbiota unbalance. Here, we tested this model by metagenomics, using black stains that threaten art conservation in Lascaux Cave. Thus, we evidenced a wide range of microbial taxa differing between black stains and neighbouring unmarked surfaces. Genes for synthesis of melanin and carotenoid pigments were more prevalent in black stains and were identified in reconstructed genomes for fungi (as expected) and bacteria. The presence of genes for degradation of aromatic compounds supports the hypothesis that recycling of chemical biocides favoured melanin-producing microorganisms. These findings extend previous predictions by revealing a wider range of microorganisms, potential biotransformations favouring pigment synthesis, as well as microbial interactions influencing microbial dynamics during cave wall alterations.

Little is known about virome changes in raw and drinking water over time, and differences between raw water sources and treatment technologies. This study used metagenomics to assess viruses prevalent in raw and drinking water samples over 1 year from six Swedish drinking water treatment plants (DWTPs) with varying treatment barriers and with different raw water sources. Sequences homologous to known viruses in the raw water samples were detected by amplification and next-generation sequencing and classified into 152 different virus species belonging to 76 virus families/orders. The majority were small bacteriophages. Other viral genomes were homologous to viruses infecting plants, invertebrates, vertebrates, mammals and giant viruses infecting amoeba or algae. Several virus species were simultaneously found in both raw and drinking water, indicating passage through the purification barriers, although reduced by 1–3 log₁₀ after treatment. Most viruses detected in water samples after ultrafiltration were small viruses, and other barriers appeared more effective at removing smaller viruses. To avoid detecting viruses possibly replicating within DWTPs, viruses were separated according to the possibility that the host could be found in the water sources or not. These results underscore the importance of monitoring both raw and drinking water for small viruses, especially when viral contamination of the source water is at risk, to ensure drinking water quality.

Anthropization of Palaeolithic caves may cause cave microbiota dysbiosis and promote the development of microbial stains on cave walls. In certain cases, chemical biocides have been used to mitigate rock alterations, but this may exacerbate microbiota unbalance. Here, we tested this model by metagenomics, using black stains that threaten art conservation in Lascaux Cave. Thus, we evidenced a wide range of microbial taxa differing between black stains and neighbouring unmarked surfaces. Genes for synthesis of melanin and carotenoid pigments were more prevalent in black stains and were identified in reconstructed genomes for fungi (as expected) and bacteria. The presence of genes for degradation of aromatic compounds supports the hypothesis that recycling of chemical biocides favoured melanin-producing microorganisms. These findings extend previous predictions by revealing a wider range of microorganisms, potential biotransformations favouring pigment synthesis, as well as microbial interactions influencing microbial dynamics during cave wall alterations.

Passive sliding motility allows Mycobacterium smegmatis to spread over soft agar surfaces. Usually, bacterial growth and reduced surface adhesion push individual bacteria outwards, resulting in circular colonies; however, more complex, dendritic colonies have also been reported. Although we could readily reproduce the circular morphotype, our non-circular colonies (hereafter digitate colonies) differed from dendritic colonies. Digitate colonies were characterised by centimetre-long, linear protrusions consisting of surface pellicle and inner biofilm components surrounding a central channel that was filled with a free-flowing suspension of M. smegmatis and aggregates. Time-lapse microscopy showed that the expansion of the fluid-filled channel resulted in lengthwise extension of the protrusions without any perceptible bacterial growth. These observations reveal a novel type of sliding motility (named hydraulic sliding) associated with a distinct colony structure and the apparent generation of force by expansion of a liquid core. The presence of a pellicle (a floating biofilm) generated without an initial liquid-air interface suggests that a previously unknown mycobacterial behaviour that could be important for colonisation and virulence has been discovered.

Passive sliding motility allows Mycobacterium smegmatis to spread over soft agar surfaces. Usually, bacterial growth and reduced surface adhesion push individual bacteria outwards, resulting in circular colonies; however, more complex, dendritic colonies have also been reported. Although we could readily reproduce the circular morphotype, our non-circular colonies (hereafter digitate colonies) differed from dendritic colonies. Digitate colonies were characterised by centimetre-long, linear protrusions consisting of surface pellicle and inner biofilm components surrounding a central channel that was filled with a free-flowing suspension of M. smegmatis and aggregates. Time-lapse microscopy showed that the expansion of the fluid-filled channel resulted in lengthwise extension of the protrusions without any perceptible bacterial growth. These observations reveal a novel type of sliding motility (named hydraulic sliding) associated with a distinct colony structure and the apparent generation of force by expansion of a liquid core. The presence of a pellicle (a floating biofilm) generated without an initial liquid-air interface suggests that a previously unknown mycobacterial behaviour that could be important for colonisation and virulence has been discovered.

Saline–alkali soils cover millions of hectares worldwide, severely limiting agricultural productivity. Although various remediation strategies have been applied, the adaptive responses of microbial communities to these interventions remain poorly understood. This study investigated microbial community responses to saline–alkali stress under different remediation treatments, focusing on diversity patterns, community assembly mechanisms, network interactions and functional roles. A randomised block experiment was conducted with three treatments: untreated saline–alkaline (SA) soils, paddy–upland rotation (PUR) and organic fertiliser (OF) amendment. Both PUR and OF treatments increased the relative abundances of Bacteroidota, Acidobacteriota and Firmicutes, indicating enrichment of beneficial taxa. Specialists exhibited higher connectivity with other microbial species than generalists, emphasising their role in stabilising indigenous microbiota and enhancing resistance to saline–alkali stress. Community assembly was dominated by deterministic processes for specialists in SA and PUR soils, while stochastic processes prevailed in other contexts across both generalists and specialists. These results reveal distinct but complementary roles of microbial generalists and specialists in soil adaptation and highlight the mechanisms by which amendments shape microbial community structure and function. Our findings provide mechanistic insights into microbial contributions to saline–alkali soil remediation, informing strategies for sustainable soil restoration.

A growing body of evidence suggests that fungi play an essential role in the decomposition process of deadwood. However, the dynamic pattern of fungal community assembly in deadwood remains poorly understood. Here, we employed a ‘space-for-time’ substitution approach in the local forest to track shifts in the deadwood mycobiota during decay. The results indicated that fungal community diversity increased from decay classes I to III, then decreased from decay classes III to IV. A high degree of structural similarity in fungal communities could occur between decay classes I and II, or decay classes III and IV. Fungal community assembly in decay classes III and IV was more governed by stochastic processes than in decay classes I and II. Moreover, we identified the six most important biomarkers and established a model that associates these biomarkers with decay classes using a random forest analysis. The chemical properties of deadwood substrates were determined to be the important driver of fungal community assembly and diversity. Our work provides novel insights into changes and the generation of fungal communities within deadwood.

The diversity of environmental yeast communities is underestimated in tropical and sub-tropical regions. Numerous studies demonstrated that human activity can alter the yeast diversity and increase pathogenic yeast proportions, indicating that people who frequently visit those areas are at risk of being infected. The main purpose of this study was to investigate the abundance and diversity of yeasts obtained from recreation areas in Bangkok. In this study, 158 soil and water samples were collected from 12 public parks. The analysis of the yeast communities revealed different patterns among recreation areas. Moreover, we aimed to identify yeasts using the internal transcribed spacer (ITS) region. Yeast isolates were identified into 22 genera, with Candida being the most common. Although the ITS region may be used to distinguish yeasts at the genus level, some isolates remain unidentified. Thus, our findings are the first report highlighting the diversity of yeast from recreation areas in Bangkok. Our study also provides information on the ITS region for environmental yeast identification, suggesting that this region might be appropriate for some yeast taxa. In conclusion, this study proposes that the abundance and diversity of yeast may differ due to several factors, such as the surrounding environment, park landscapes, and water supplies for park maintenance.

Plastic waste is a mounting global problem with over 400 million tons of plastic produced annually and over 50% ending up in landfill after its intended use. Two types of plastics are particularly problematic and are difficult to recycle: low-density polyethylene (LDPE) and polyurethane (PU). Fortuitously, nature may offer a potential solution; Galleria mellonella larvae can digest various plastics, including LDPE, which is believed to be driven by microbes in their gut microbiome. Although some studies have examined their gut microbiota on a metagenomic level, little is known about their ability to degrade plastics. Here, we isolated six bacterial strains from G. mellonella larvae feeding on LDPE. One of them, identified as Bacillus subtilis GM_03, has the capacity to break down commercial PU (Impranil), in addition to LDPE. This bacterium encodes a suite of genes required for plastic degradation. Directed evolution was used to enhance this strain's plastic degrading rate by over six-fold. Sequencing of the evolved culture revealed four genes, srfAB, fadD, appA and citS, associated with this increased PU degradation rate. This is the first time that B. subtilis isolated from G. mellonella larvae has been shown to be capable of degrading multiple types of plastics.