The soil environment is essential to many ecosystem services which are primarily mediated by microbial communities. Soil physical and chemical conditions are altered on local and global scales by anthropogenic activity and which threatens the provision of many soil services. Despite the importance of soil biota for ecosystem function, we have limited ability to predict and manage soil microbial community responses to change. To better understand causal relationships between microbial community structure and ecological function, we argue for a systems approach to prediction and management of microbial response to environmental change. This necessitates moving beyond concepts of resilience, resistance and redundancy that assume single optimum stable states, to ones that better reflect the dynamic and interactive nature of microbial systems. We consider the response of three soil groups (ammonia oxidisers, denitrifiers, symbionts) to anthropogenic perturbation to motivate our discussion. We also present a network re‐analysis of a saltmarsh microbial community which illustrates how such approaches can reveal ecologically important connections between functional groups. More generally, we suggest the need for integrative studies which consider how environmental variables moderate interactions between functional groups, how this moderation affects biogeochemical processes and how these feedbacks ultimately drive ecosystem services provided by soil biota.

Background. Microbial inhabitants of soils are important to ecosystem and planetary functions, yet there are large gaps in our knowledge of their diver

Ex situ microelectrode experiments, using cyanobacterial biofilms from karst water creeks, were conducted under various pH, temperature, and constant-alkalinity conditions to investigate the effects of changing environmental parameters on cyanobacterial photosynthesis-induced calcification. Microenvironmental chemical conditions around calcifying sites were controlled by metabolic activity over a wide range of photosynthesis and respiration rates, with little influence from overlying water conditions. Regardless of overlying water pH levels (from 7.8 to 8.9), pH at the biofilm surface was approximately 9.4 in the light and 7.8 in the dark. The same trend was observed at various temperatures (4°C and 17°C). Biological processes control the calcium carbonate saturation state (Ω) in these and similar systems and are able to maintain Ω at approximately constant levels over relatively wide environmental fluctuations. Temperature did, however, have an effect on calcification rate. Calcium flux in this system is limited by its diffusion coefficient, resulting in a higher calcium flux (calcification and dissolution) at higher temperatures, despite the constant, biologically mediated pH. The ability of biological systems to mitigate the effects of environmental perturbation is an important factor that must be considered when attempting to predict the effects of increased atmospheric partial CO₂pressure on processes such as calcification and in interpreting microfossils in the fossil record.

The success of environmental DNA (eDNA) approaches for species detection has revolutionized biodiversity monitoring and distribution mapping. Targeted eDNA amplification approaches, such as quantitative PCR, have improved our understanding of species distribution, and metabarcoding‐based approaches have enabled biodiversity assessment at unprecedented scales and taxonomic resolution. eDNA datasets, however, are often scattered across repositories with inconsistent formats, varying access restrictions, and inadequate metadata; this limits their interoperation, reuse, and overall impact. Adopting FAIR (Findable, Accessible, Interoperable, and Reusable) data practices with eDNA data can transform the monitoring of biodiversity and individual species and support data‐driven biodiversity management across broad scales. FAIR practices remain underdeveloped in the eDNA community, partly due to gaps in adapting existing vocabularies, such as Darwin Core (DwC) and Minimum Information about any (x) Sequence (MIxS), to eDNA‐specific needs and workflows. To address these challenges, we propose a comprehensive FAIR eDNA (FAIRe) Metadata Checklist, which integrates existing data standards and introduces new terms tailored to eDNA workflows. Metadata are systematically linked to both raw data (e.g., metabarcoding sequences, Ct/Cq values of targeted qPCR assays) and derived biological observations (e.g., Amplicon Sequence Variant (ASV)/Operational Taxonomic Unit (OTU) tables, species presence/absence). Along with formatting guidelines, tools, templates, and example datasets, we introduce a standardized, ready‐to‐use approach for FAIR eDNA practices. Through broad collaboration, we seek to integrate these guidelines into established biodiversity and molecular data standards, promote journal data policies, and foster user‐driven improvements and uptake of FAIR practices among eDNA data producers. In proposing this standardized approach and developing a long‐term plan with key databases and data standard organizations, the goal is to enhance accessibility, maximize reuse, and elevate the scientific impact of these valuable biodiversity data resources.