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The rapid evolution of microbiology as a field of research has led to the introduction of new terminology and the adaptation of existing terms. However, inconsistencies in the use of these terms, including variations across different scientific disciplines, can lead to confusion and miscommunication within the scientific community. This article discusses the importance of precise terminology in microbiome research, highlighting examples where terms have been misused or redefined without clear justification. We also present a list of frequently used terms in microbial ecology along with their specific definitions. We argue that the misuse of terminology can hinder scientific progress bymore » creating ambiguity and misunderstanding. To address this, we propose a set of guidelines for the consistent use of key terms and provide clear definitions for some of the most commonly misused or newly introduced terms in the field. The definitions provided herein will also function as a guide for young researchers new to the field of microbial ecology. Accurate and consistent use of terminology is crucial for effective communication and collaboration in microbiology research. By adhering to standardised definitions, researchers can ensure that their work is clearly communicated and contributes meaningfully to the progress of science.« less

Anthropogenic-driven climate change is accelerating permafrost thaw, threatening to release vast carbon stores through increased microbial activity. While microbial roles are increasingly studied, the contributions of viruses remain largely unexplored, in part due to soil-associated technical challenges that have hindered their detection and characterization. Here, we applied an optimized virion enrichment workflow along a permafrost thaw gradient, identifying 9,963 viral populations (vOTUs), including single- and double-stranded DNA viruses, with 99.9% novelty compared to other soils. Hosts were predicted for 38% of vOTUs, spanning nine archaeal, and 36 bacterial phyla, 22% of which were linked to metagenome-assembled genomes, including key carbon-cyclingmore » taxa. Genomic analyses revealed 811 putative auxiliary metabolic genes (AMGs) from 658 vOTUs, nearly half involved in carbon processing. These included 59 glycoside hydrolases (GH) across nine GH families, 45 for monosaccharide degradation, and seven involved in short-chain fatty acid and C1 metabolism, linking viruses to both early and late stages of carbon turnover. Additionally, six vOTUs carried racD, which may stabilize microbial necromass and promote long-term carbon storage. Viral and AMG functional diversity increased with thaw stage, indicating that viruses might participate in a broadening range of microbial metabolic processes as permafrost thaws. These findings expand our understanding of virus contributions in microbial carbon processing and suggest their important role in deciphering soil carbon fate under changing climate conditions.« less

Understanding the spatiotemporal dynamics of microbial communities is essential for predicting their ecological roles and interactions with host plants. In a recent study, Wei and colleagues (Microbiol Spectr 13:e02097-24, 2024) investigated fungal diversity across multiple plant and soil compartments in rubber trees over two seasons and two geographically distinct regions in China. Their findings revealed that alpha diversity was primarily influenced by seasonal changes and physicochemical factors, while beta diversity exhibited a strong geographical pattern, shaped by leaf phosphorus and soil available potassium. These results highlight the role of environmental drivers in shaping within-community diversity, while other factors contribute tomore » the differences between fungal communities across the soil–plant continuum. By distinguishing the effects of temporal and spatial factors, this study provides detailed insights into plant-associated microbiomes and emphasizes the need for further research on the functional implications of microbial diversity in the context of changing environmental and agricultural conditions.« less

The interdisciplinary nature of microbiome research, coupled with the generation of complex multi-omics data, makes knowledge sharing challenging. The Strengthening the Organization and Reporting of Microbiome Studies (STORMS) guidelines provide a checklist for the reporting of study information, experimental design and analytical methods within a scientific manuscript on human microbiome research. Here, in this Consensus Statement, we present the standards for technical reporting in environmental and host-associated microbiome studies (STREAMS) guidelines. The guidelines expand on STORMS and include 67 items to support the reporting and review of environmental (for example, terrestrial, aquatic, atmospheric and engineered), synthetic and non-human host-associated microbiomemore » studies in a standardized and machine-actionable manner. Based on input from 248 researchers spanning 28 countries, we provide detailed guidance, including comparisons with STORMS, and case studies that demonstrate the usage of the STREAMS guidelines. In conclusion, STREAMS, like STORMS, will be a living community resource updated by the Consortium with consensus-building input of the broader community.« less

Ecology, evolution, and biodiversity of microbiomes and viromes in extreme environments are key areas of research that explore how microbial communities adapt, survive, and thrive under harsh conditions. The studies published in our Research Topic advance our understanding of microbial and viral diversity, evolutionary processes, and the ecological roles of these communities, with implications for biotechnology, climate resilience, and even astrobiology.

Anaerobic incubations of peat have been widely used to explore soil processes, but this in vitro technique raises many questions as to how well it reproduces in situ conditions. To investigate this, we conducted 60–100 days (+25 days pre‐incubation) anaerobic, temperature‐controlled incubation experiments across a temperature range of 1–26°C on samples from bog and fen habitats, at two different depths (9–19 and 25–35 cm). Here, we observed exponential increases in CO₂ and methane production with temperature in all conditions. We then compared field‐based measurements of methane emission with modeled expectations by extrapolating incubation‐determined methane production rates based on (a) soilmore » temperature profiles, (b) the observed incubation temperature‐methane production relationship, and (c) seasonal thaw depth from each site. The resulting incubation‐extrapolated methane production agreed with measured emission rates within a factor of two at both sites and corresponded to 182 ± 54% and 59 ± 14% of the measured average yearly fluxes from the field for the bog and fen, respectively. The underestimation of fen methane fluxes may be due to the lack of living plant root‐derived dissolved organic carbon inputs in incubations, a key process in fens. Conversely, the overestimation in bogs could be attributed to methane oxidation in the field, which is absent in anaerobic incubation conditions. Nonetheless incubations predicted greenhouse gas emissions from a northern peatland within a factor of two.« less

Soil virus ecology is an exciting but still nascent field of research in soil microbiology. While there has been a recent surge in soil virus research studies, many fundamental questions remain unanswered, and a range of technical and bioinformatic challenges need to be overcome. In this perspective article, we present a series of key questions that highlight fruitful research areas for ongoing and future efforts. These include describing the challenges involved in understanding soil viral abundance and activity, spatiotemporal dynamics, life strategy prevalence, virus-mediated biogeochemical impacts, viral protein function, host prediction, and soil RNA virus discovery. In the near term,more » combining approaches (e.g., cultivation-based, meta-omics, biogeochemical, experimental, and bioinformatic) will be key to assessing the ecological and biogeochemical impacts of soil viruses from the microscopic to the field and global scales. Still, we stress that results must be tempered by current methodological limitations and highlight knowledge gaps that are most pressing to fill via new methods or measurements, such as the prevalence of different viral replication strategies across soils, the fate of microbial necromass carbon after viral lysis, the frequency of virus-host encounters that do not lead to successful infections yet could be bioinformatically mistaken as infections, and the diversity and ecological impacts of RNA viruses in soil.« less

Soil rewetting after a dry period results in a surge of activity and succession in both microbial and DNA virus communities. Less is known about the response of RNA viruses to soil rewetting—while they are highly diverse and widely distributed in soil, they remain understudied. We hypothesized that RNA viruses would show temporal succession following rewetting and that phosphate amendment would influence their trajectory, as viral proliferation may cause phosphorus limitation. Using 39 time-resolved metatranscriptomes and amplicon data, 2190 RNA viral populations were identified across five phyla, with 26 % of these predicted to infect bacteria, and 11 % fungi.more » Only 1.2 % of viral populations had annotated capsid genes, suggesting most persist via intracellular replication without a free virion phase. Phosphate amendment altered RNA viral community composition within the first week and amended vs. unamended communities remained distinguishable for up to three weeks. While the overall host community remained stable, certain bacterial populations showed reduced abundance in phosphate-amended soils, likely due to increased viral lysis, as RNA bacteriophages proliferated significantly. Notably, 60 % of the viruses with increased abundance under phosphate amendment belonged to basal Lenarviricota clades rather than well-known groups like Leviviricetes. We estimate RNA bacteriophage infections may affect 10⁷–10⁹ bacteria per gram of soil, aligning with the total bacterial population (10⁷–10¹⁰ g^-1 soil), suggesting that RNA phages significantly influence bacterial communities post-wet-up, with phosphorus availability modulating this effect.« less

The research field of soil viral ecology continues to advance rapidly as the roles of viruses in the functioning of soil ecosystems are increasingly recognized. To address recent developments in the field, the second International Soil Virus Conference was held in Livermore, California, USA, from June 25 to 27th, 2024, providing soil viral ecologists the opportunity to share new findings and suggest guidelines for future research, while encouraging international scientific discussion and collaboration. The meeting was held in person with sessions simultaneously streamed online. Fifty researchers attended from ten different countries and spanned a wide range of subfields and careermore » stages. A total of 21 oral presentations were presented, followed by discussions covering key themes in soil viral research. This report summarizes the main takeaways and recommendations from the talks and discussions.« less

The soil microbiome is recognized as an essential component of healthy soils. Viruses are also diverse and abundant in soils, but their roles in soil systems remain unclear. Here we argue for the consideration of viruses in soil microbial food webs and describe the impact of viruses on soil biogeochemistry. The soil food web is an intricate series of trophic levels that span from autotrophic microorganisms to plants and animals. Each soil system encompasses contrasting and dynamic physicochemical conditions, with labyrinthine habitats composed of particles. Conditions are prone to shifts in space and time, and this variability can obstruct ormore » facilitate interactions of microorganisms and viruses. Because viruses can infect all domains of life, they must be considered as key regulators of soil food web dynamics and biogeochemical cycling. Finally, we highlight future research avenues that will enable a more robust understanding of the roles of viruses in soil function and health.« less