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

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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 freshwater–ecosystem 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. This article is categorized under: Water and Life > Methods Water and Life > Nature of Freshwater Ecosystems
A schematic diagram of some of the most frequently used molecular and “omics” methods, along with the types of research questions they are suitable to address. Whether the study is observational, experimental, or routine biomonitoring, all approaches require the extraction and purification of biological molecules, such as DNA or RNA from the environment. Approaches on the left require amplification of specific genes via PCR, whereas approaches on the right do not require a target, and are conducted on the entire pool of nucleic acids
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A graphical abstract for each of the case‐studies presented here. (a) Thompson et al. () used qPCR analysis of the opd gene to show that the abundance of pesticide degrading microorganisms increased sevenfold in contaminated sediments, relative to control sediments. (b) Lansdown et al. () conducted metagenetic sequencing of anammox (hzo) genes from riverbed sediments of different underlying geology. They discovered four distinct phylogenetic clades of anammox bacteria that differed markedly in relative abundance across the different riverbed geologies. (c) Vila‐Costa, Sharma, Moran, and Casamayor () performed metatranscriptomic sequencing of lake plankton across a diel cycle. Notably, they found that phosphate uptake genes were differentially expressed according to the source of phosphate, and time of day
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