Streams of data from drops of water: 21st century molecular microbial ecology

Abstract

Microorganisms are ubiquitous and represent a taxonomically and functionally diverse component of freshwater environments of significant ecological importance. The bacteria, archaea, and microbial eukarya in freshwater systems support a range of ecosystem processes and functions, including mediating all major biogeochemical cycles, and therefore regulate the flow of multiple ecosystem services. Yet relative to conspicuous higher taxa, microbial ecology remains poorly understood. As the anthropocene progresses, the demand for freshwaterecosystem services is both increasing with growing human population density, and by association, increasingly threatened from multiple and often interacting stressors, such as climate change, eutrophication, and chemical pollution. Thus, it is imperative to understand the ecology of microorganisms and their functional role in freshwater ecosystems if we are to manage the future of these environments effectively. To do this, researchers have developed a vast array of molecular tools that can illuminate the diversity, composition, and activity of microbial communities. Within this primer, we discuss the history of molecular approaches in microbial ecology, and highlight the scope of questions that these methods enable researchers to address. Using some recent case studies, we describe some exemplar research into the microbial ecology of freshwater systems, and emphasize how molecular methods can provide novel ecological insights. Finally, we detail some promising developments within this research field, and how these might shape the future research landscape of freshwater microbial ecology.

What drives study‐dependent differences in distance–decay relationships of microbial communities?

“…Although the context in which a study was undertaken might contribute to variability in microbial distance–decay relationships, so too could different methodologies. Technological advances have yielded new insight into the structure and functioning of the development of environmental microbial communities (Clark et al., 2018). However, rapid turnover in molecular methodologies means that our perception of microbial β‐diversity patterns integrates methods that vary substantially in both coverage (ability to detect a greater proportion of the community in a given sample) and resolution (ability to resolve closely related taxa) (Glenn, 2011; Muyzer, 1999).…”

Trophic Status Is Associated With Community Structure and Metabolic Potential of Planktonic Microbiota in Plateau Lakes

“…The microbiota in aquatic ecosystems plays an important role in elemental cycling and global energy fluxes (Falkowski et al, 2008; Clark et al, 2018; Cronan, 2018). The relations between the taxonomic structure of microbial communities in aquatic environments and complex environmental factors such as trophic status (Llirós et al, 2014; Wan et al, 2017), seasons (Zhu et al, 2019), elevation gradient (Li H. et al, 2017), and salinity (Eiler et al, 2014) have been well studied.…”

Seasonal epiphytic microbial dynamics on grapevine leaves under biocontrol and copper fungicide treatments

“…Next-generation sequencing (NGS) and quantitative PCR (qPCR) techniques facilitate rapid and cost-competitive mapping of complex microbiomes by tracking fastidious, unculturable or even unknown taxa and their roles 22,23 . In particular, through accurate, real-time enumeration of taxonomic or functional gene markers, qPCR has enabled microbiologists to quantify specific species or phylotypes out of an environmental "genetic soup" 23 . Nonetheless, qPCR assays rely exclusively on known genes and thus overlook taxa distinct from those already described 24 .…”