Diversity begets diversity: chemical and microbial diversity co-vary in freshwater to influence ecosystem functioning

Invisible to the naked eye lies a tremendous diversity of organic molecules and organisms that make major contributions to important biogeochemical cycles. However, how the diversity and composition of these two communities are inter-linked remains poorly characterised in freshwaters, despite the potential for chemical and microbial diversity to promote one another. Here we exploited gradients in chemodiversity within a common microbial pool to test how chemical and biological diversity covary and characterized the implications for ecosystem functioning. We found that both chemodiversity and genes associated with organic matter decomposition increased as more plant litterfall accumulated in experimental lake sediments, consistent with scenarios of future environmental change. Chemical and microbial diversity were also positively correlated, with dissolved organic matter having stronger effects on microbes than vice versa. Under our experimental scenarios that increased sediment organic matter from 5 to 25% or darkened overlying waters by 2.5-times, the resulting increases in chemodiversity could increase greenhouse gas concentrations in lake sediments by an average of 1.5- to 2.7-times, when all the other effects of litterfall and water color were considered. Our results open a major new avenue for research in aquatic ecosystems by exposing connections between chemical and microbial diversity and their implications for the global carbon cycle in greater detail than ever before.Funding came from a Natural Environment Research Council grant NE/L006561/1 to AJT and a Gates Cambridge Scholarship to AF

Feasting on terrestrial organic matter: Dining in a dark lake changes microbial decomposition.

Boreal lakes are major components of the global carbon cycle, partly because of sediment-bound heterotrophic microorganisms that decompose within-lake and terrestrially derived organic matter (t-OM). The ability for sediment bacteria to break down and alter t-OM may depend on environmental characteristics and community composition. However, the connection between these two potential drivers of decomposition is poorly understood. We tested how bacterial activity changed along experimental gradients in the quality and quantity of t-OM inputs into littoral sediments of two small boreal lakes, a dark and a clear lake, and measured the abundance of operational taxonomic units and functional genes to identify mechanisms underlying bacterial responses. We found that bacterial production (BP) decreased across lakes with aromatic dissolved organic matter (DOM) in sediment pore water, but the process underlying this pattern differed between lakes. Bacteria in the dark lake invested in the energetically costly production of extracellular enzymes as aromatic DOM increased in availability in the sediments. By contrast, bacteria in the clear lake may have lacked the nutrients and/or genetic potential to degrade aromatic DOM and instead mineralized photo-degraded OM into CO2 . The two lakes differed in community composition, with concentrations of dissolved organic carbon and pH differentiating microbial assemblages. Furthermore, functional genes relating to t-OM degradation were relatively higher in the dark lake. Our results suggest that future changes in t-OM inputs to lake sediments will have different effects on carbon cycling depending on the potential for photo-degradation of OM and composition of resident bacterial communities

Fifty important research questions in microbial ecology.

Microbial ecology provides insights into the ecological and evolutionary dynamics of microbial communities underpinning every ecosystem on Earth. Microbial communities can now be investigated in unprecedented detail, although there is still a wealth of open questions to be tackled. Here we identify 50 research questions of fundamental importance to the science or application of microbial ecology, with the intention of summarising the field and bringing focus to new research avenues. Questions are categorised into seven themes: host-microbiome interactions; health and infectious diseases; human health and food security; microbial ecology in a changing world; environmental processes; functional diversity; and evolutionary processes. Many questions recognise that microbes provide an extraordinary array of functional diversity that can be harnessed to solve real-world problems. Our limited knowledge of spatial and temporal variation in microbial diversity and function is also reflected, as is the need to integrate micro- and macro-ecological concepts, and knowledge derived from studies with humans and other diverse organisms. Although not exhaustive, the questions presented are intended to stimulate discussion and provide focus for researchers, funders and policy makers, informing the future research agenda in microbial ecology.This work was supported by contributions from the British Ecological Society and the University of Salford towards funding the workshop. KMF was funded by the Finnish Cultural Foundation, NLMF Colciencias, MCM by Earth and Life Systems Alliance, and WJS by Arcadi

Host genetic determinants of spontaneous hepatitis C clearance

Acute infection with the hepatitis C virus (HCV) induces a wide range of innate and adaptive immune responses. A total of 20-50% of acutely HCV-infected individuals permanently control the virus, referred to as 'spontaneous hepatitis C clearance', while the infection progresses to chronic hepatitis C in the majority of cases. Numerous studies have examined host genetic determinants of hepatitis C infection outcome and revealed the influence of genetic polymorphisms of human leukocyte antigens, killer immunoglobulin-like receptors, chemokines, interleukins and interferon-stimulated genes on spontaneous hepatitis C clearance. However, most genetic associations were not confirmed in independent cohorts, revealed opposing results in diverse populations or were limited by varying definitions of hepatitis C outcomes or small sample size. Coordinated efforts are needed in the search for key genetic determinants of spontaneous hepatitis C clearance that include well-conducted candidate genetic and genome-wide association studies, direct sequencing and follow-up functional studies

The CALeDNA program: Citizen scientists and researchers inventory California’s biodiversity

Climate change is leading to habitat shifts that threaten species persistence throughout California’s unique ecosystems. Baseline biodiversity data would provide opportunities for habitats to be managed under short-term and long-term environmental change. Aiming to provide biodiversity data, the UC Conservation Genomics Consortium launched the California Environmental DNA (CALeDNA) program to be a citizen and community science biomonitoring initiative that uses environmental DNA (eDNA, DNA shed from organisms such as from fur, feces, spores, pollen or leaves). Now with results from 1,000 samples shared online, California biodiversity patterns are discoverable. Soil, sediment and water collected by researchers, undergraduates and the public reveal a new catalog of thousands of organisms that only slightly overlap with traditional survey bioinventories. The CALeDNA website lets users explore the taxonomic diversity in different ways, and researchers have created tools to help people new to eDNA to analyze community ecology patterns. Although eDNA results are not always precise, the program team is making progress to fit it into California’s biodiversity management toolbox, such as for monitoring ecosystem recovery after invasive species removal or wildfire

Make EU trade with Brazil sustainable

Brazil, home to one of the planet's last great forests, is currently in trade negotiations with its second largest trading partner, the European Union (EU). We urge the EU to seize this critical opportunity to ensure that Brazil protects human rights and the environment