@article{FaschingAkotoyeBižićetal.2020,
  author    = {Fasching, Christina and Akotoye, Christian and Bižić, Mina and Fonvielle, Jeremy Andre and Ionescu, Danny and Mathavarajah, Sabateeshan and Zoccarato, Luca and Walsh, David A. and Grossart, Hans-Peter and Xenopoulos, Marguerite A.},
  title     = {Linking stream microbial community functional genes to dissolved organic matter and inorganic nutrients},
  series = {Limnology and oceanography},
  volume    = {65},
  journal   = {Limnology and oceanography},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {0024-3590},
  doi       = {10.1002/lno.11356},
  pages     = {S71 -- S87},
  year      = {2020},
  abstract  = {There is now increasing evidence for the importance of microbial regulation of biogeochemical cycling in streams. Resource availability shapes microbial community structure, but less is known about how landscape-mediated availability of nutrients and carbon can control microbial functions in streams. Using comparative metagenomics, we examined the relationship between microbial functional genes and composition of dissolved organic matter (DOM), nutrients, and suspended microbial communities in 11 streams, divided into three groups based on the predominant land cover category (agriculture, forested, or wetland). Using weighted gene co-occurrence network analysis, we identified clusters of functions related to DOM composition, agricultural land use, and/or wetland and forest land cover. Wetland-dominated streams were characterized by functions related to nitrogen metabolism and processing of aromatic carbon compounds, with strong positive correlations with dissolved organic carbon concentration and DOM aromaticity. Forested streams were characterized by metabolic functions related to monomer uptake and carbohydrates, such as mannose and fructose metabolism. In agricultural streams, microbial functions were correlated with more labile, protein-like DOM, PO4, and NO3, likely reflecting functional adaptation to labile DOM and higher nutrient concentrations. Distinct changes in the functional composition and loss of functional diversity of microorganisms became evident when comparing natural to agricultural catchments. Although all streams showed signs of functional redundancy, loss of species richness per function in agricultural catchments suggests that microbial functions in natural catchments may be more resilient to disturbance. Our results provide new insight into microbial community functions involved in nutrient and carbon biogeochemical cycles and their dependence on specific environmental settings.},
  language  = {en}
}
@article{GrossartMassanaMcMahonetal.2019,
  author    = {Grossart, Hans-Peter and Massana, Ramon and McMahon, Katherine D. and Walsh, David A.},
  title     = {Linking metagenomics to aquatic microbial ecology and biogeochemical cycles},
  series = {Limnology and oceanography},
  volume    = {65},
  journal   = {Limnology and oceanography},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {0024-3590},
  doi       = {10.1002/lno.11382},
  pages     = {S2 -- S20},
  year      = {2019},
  abstract  = {Microbial communities are essential components of aquatic ecosystems through their contribution to food web dynamics and biogeochemical processes. Aquatic microbial diversity is immense and a general challenge is to understand how metabolism and interactions of single organisms shape microbial community dynamics and ecosystem-scale biogeochemical transformations. Metagenomic approaches have developed rapidly, and proven to be powerful in linking microbial community dynamics to biogeochemical processes. In this review, we provide an overview of metagenomic approaches, followed by a discussion on some recent insights they have provided, including those in this special issue. These include the discovery of new taxa and metabolisms in aquatic microbiomes, insights into community assembly and functional ecology as well as evolutionary processes shaping microbial genomes and microbiomes, and the influence of human activities on aquatic microbiomes. Given that metagenomics can now be considered a mature technology where data generation and descriptive analyses are relatively routine and informative, we then discuss metagenomic-enabled research avenues to further link microbial dynamics to biogeochemical processes. These include the integration of metagenomics into well-designed ecological experiments, the use of metagenomics to inform and validate metabolic and biogeochemical models, and the pressing need for ecologically relevant model organisms and simple microbial systems to better interpret the taxonomic and functional information integrated in metagenomes. These research avenues will contribute to a more mechanistic and predictive understanding of links between microbial dynamics and biogeochemical cycles. Owing to rapid climate change and human impacts on aquatic ecosystems, the urgency of such an understanding has never been greater.},
  language  = {en}
}