Do-it-Yourself Mock Community Standard for Multi-Step Assessment of Microbiome Protocols

Arrive and wait: Inactive bacterial taxa contribute to perceived soil microbiome resilience after a multidecadal press disturbance

Long-term (press) disturbances like the climate crisis and other anthropogenic pressures are fundamentally altering ecosystems and their functions. Many critical ecosystem functions, such as biogeochemical cycling, are facilitated by microbial communities. Understanding the functional consequences of microbiome responses to press disturbances requires ongoing observations of the active populations that contribute to functions. This study leverages a 7-year time series of a 60-year-old coal seam fire (Centralia, Pennsylvania, USA) to examine the resilience of soil bacterial microbiomes to a press disturbance. Using 16S rRNA and 16S rRNA gene amplicon sequencing, we assessed the interannual dynamics of the active subset and the 'whole' bacterial community. Contrary to our hypothesis, the whole communities demonstrated greater resilience than active subsets, suggesting that inactive members contributed to overall structural resilience. Thus, in addition to selection mechanisms of active populations, perceived microbiome resilience is also supported by mechanisms of dispersal, persistence, and revival from the local dormant pool.

Considerations for the inclusion of metabarcoding data in the plant protection product risk assessment of the soil microbiome

There is increasing interest in further developing the plant protection product (PPP) environmental risk assessment, particularly within the European Union, to include the assessment of soil microbial community composition, as measured by metabarcoding approaches. However, to date, there has been little discussion as to how this could be implemented in a standardized, reliable, and robust manner suitable for regulatory decision-making. Introduction of metabarcoding-based assessments of the soil microbiome into the PPP risk assessment would represent a significant increase in the degree of complexity of the data that needs to be processed and analyzed in comparison to the existing risk assessment on in-soil organisms. The bioinformatics procedures to process DNA sequences into community compositional data sets currently lack standardization, while little information exists on how these data should be used to generate regulatory endpoints and the ways in which these endpoints should be interpreted. Through a thorough and critical review, we explore these challenges. We conclude that currently, we do not have a sufficient degree of standardization or understanding of the required bioinformatics and data analysis procedures to consider their use in an environmental risk assessment context. However, we highlight critical knowledge gaps and the further research required to understand whether metabarcoding-based assessments of the soil microbiome can be utilized in a statistically and ecologically relevant manner within a PPP risk assessment. Only once these challenges are addressed can we consider if and how we should use metabarcoding as a tool for regulatory decision-making to assess and monitor ecotoxicological effects on soil microorganisms within an environmental risk assessment of PPPs. Integr Environ Assess Manag 2024;20:337-358. © 2023 SETAC.

Revealing the Tick Microbiome: Insights into Midgut and Salivary Gland Microbiota of Female Ixodes ricinus Ticks

The ectoparasite Ixodes ricinus is an important vector for many tick-borne diseases (TBD) in the northern hemisphere, such as Lyme borreliosis, rickettsiosis, human granulocytic anaplasmosis, or tick-borne encephalitis virus. As climate change will lead to rising temperatures in the next years, we expect an increase in tick activity, tick population, and thus in the spread of TBD. Consequently, it has never been more critical to understand relationships within the microbial communities in ticks that might contribute to the tick's fitness and the occurrence of TBD. Therefore, we analyzed the microbiota in different tick tissues such as midgut, salivary glands, and residual tick material, as well as the microbiota in complete Ixodes ricinus ticks using 16S rRNA gene amplicon sequencing. By using a newly developed DNA extraction protocol for tick tissue samples and a self-designed mock community, we were able to detect endosymbionts and pathogens that have been described in the literature previously. Further, this study displayed the usefulness of including a mock community during bioinformatic analysis to identify essential bacteria within the tick.