Coupling biogeochemical process rates and metagenomic blueprints of coastal bacterial assemblages in the context of environmental change

Abstract

Bacteria are major drivers of biogeochemical nutrient cycles and energy fluxes in marine environments, yet how bacterial communities respond to environmental change is not well known. Metagenomes allow examination of genetic responses of the entire microbial community to environmental change. However, it is challenging to link metagenomes directly to biogeochemical process rates. Here, we investigate metagenomic responses in natural bacterioplankton communities to simulated environmental stressors in the Baltic Sea, including increased river water input, increased nutrient concentration, and reduced oxygen level. This allowed us to identify informative prokaryotic gene markers, responding to environmental perturbation. Our results demonstrate that metagenomic and metabolic changes in bacterial communities in response to environmental stressors are influenced both by the initial community composition and by the biogeochemical factors shaping the functional response. Furthermore, the different sources of dissolved organic matter (DOM) had the largest impact on metagenomic blueprint. Most prominently, changes in DOM loads influenced specific transporter types reflecting the substrate availability and DOC assimilation and consumption pathways. The results provide new knowledge for developing models of ecosystem structure and biogeochemical cycling in future climate change scenarios and advance our exploration of the potential use of marine microorganisms as markers for environmental conditions.

Effects of allochthonous dissolved organic matter input on microbial composition and nitrogen-cycling genes at two contrasting estuarine sites

“…To compare the bacterial communities, the taxonomic richness (calculated as abundance-based coverage estimator (ACE)) and the Shannon diversity index were estimated (Markussen et al, 2018). Significant differences (P<0.05) between bacterial abundance and production data were tested using Dunnett´s test (Markussen et al, 2018).…”

“…To compare the bacterial communities, the taxonomic richness (calculated as abundance-based coverage estimator (ACE)) and the Shannon diversity index were estimated (Markussen et al, 2018). Significant differences (P<0.05) between bacterial abundance and production data were tested using Dunnett´s test (Markussen et al, 2018). Raw counts of EC/PFAM/COGs were normalized to counts per million (cpm) using EdgeR (Robinson et al, 2010) to test for significant differences in COG abundances between control samples and treatments.…”

“…Experimental setup for Exp I and Exp II The setup described here was part of a larger experiment reported elsewhere (Markussen et al, 2018). Microcosm experiments with the same setup were conducted at the Marine Biological Laboratory (University of Copenhagen, Denmark) using Øresund water (Exp I) and at the Tvärminne Zoological Field station (University of Helsinki, Finland) using water from Storfjärden, Gulf of Finland (Exp II).…”

“…Data were adapted from Markussen et al (2018). Briefly, Samples for bacterial enumeration were fixed with glutaraldehyde (1% final conc., Sigma-Aldrich), stored at -80°C, and later enumerated using SYBR green I (Invitrogen) and a BD FACS Canto II flow cytometer.…”

Soil biodiversity and biogeochemical function in managed ecosystems

“…Soil organisms play a vital role in many important ecosystem functions that influence soil and crop productivity and system sustainability. Microbial communities are the main drivers of biogeochemical cycles, therefore changes in their abundance, activity, and community structure may affect nutrient flows in soil (Schmidt et al 2011;Markussen et al 2018). This includes direct processes such as crop decomposition, nutrient mineralisation and mobilisation, denitrification, and nitrogen (N) fixation, in addition to cascades of impacts (C and nutrient flow) throughout the soil food web (Fig.…”