Dalcin Martins, P. | bioRxiv Science

bioRxiv2021

Unraveling nitrogen, sulfur and carbon metabolic pathways and microbial community transcriptional responses to substrate deprivation and toxicity stresses in a bioreactor mimicking anoxic brackish coastal sediment conditions

Microbial communities are key drivers of carbon, sulfur and nitrogen cycling in coastal ecosystems, where they are subjected to dynamic shifts in substrate availability and exposure to toxic compounds. However, how these shifts affect microbial interactions and function is poorly understood. Unraveling such microbial community responses is key to understand their environmental distribution and resilience under current and future disturbances. Here, we used metagenomics and metatranscriptomics to investigate microbial community structure and transcriptional responses to prolonged ammonium deprivation and sulfide and nitric oxide toxicity stresses in a controlled bioreactor system mimicking coastal sediment conditions. Candidatus Nitrobium versatile, identified in this study as a sulfide-oxidizing denitrifier, became a rare community member upon ammonium removal. The methanotroph Ca. Methanoperedens nitroreducens showed remarkable resilience to both experimental conditions, dominating transcriptional activity of dissimilatory nitrate reduction to ammonium (DNRA). After the ammonium removal experiment, a novel methanotroph species that we have named Ca. Methylomirabilis tolerans outcompeted Ca. Methylomirabilis lanthanidiphila and the anaerobic ammonium oxidizer (anammox) Ca. Kuenenia stuttgartiensis outcompeted Ca. Scalindua rubra. At the end of the sulfide and nitric oxide experiment, a gammaproteobacterium affiliated to the family Thiohalobacteraceae was enriched and dominated transcriptional activity of sulfide:quinone oxidoreductase. Our results indicate that some community members could be more resilient to stresses than others in coastal ecosystems, leading to dynamic microbial community shifts and novel functional states. Methane and sulfide oxidation could be ecosystem functions preserved across the investigated disturbances, while differing nitrogen cycling pathways might be favored in response to stresses. ImportanceCoastal ecosystems are primary zones of biogeochemical cycling, processing inputs of nutrients both generated in situ and derived from land runoff. Microbial communities that inhabit costal sediments perform these biogeochemical reactions, but microbial responses to dynamic, periodic substrate deprivation and exposure to toxic compounds remain elusive. In this study, we sought to address this knowledge gap in a controlled bioreactor system, unraveling microbial metabolic pathways and monitoring microbial responses to stresses that might occur in costal sediments. We identified key microbial players and shifts in their abundance and transcriptional activity. Our results indicated that methanotrophs were particularly resilient to stresses, sulfide oxidizers differed in resiliency but the community maintained sulfide oxidation function across stresses, and that anaerobic ammonium oxidizing (anammox) bacteria were sensitive to substrate deprivation but could restore activity once favorable conditions were reestablished. These insights will help to understand and predict coastal ecosystem responses to future disturbances.

microbiology↗

bioRxiv2020

Enrichment of novel Verrucomicrobia, Bacteroidetes and Krumholzibacteria in an oxygen-limited, methane- and iron-fed bioreactor inoculated with Bothnian Sea sediments

Microbial methane oxidation is a major biofilter preventing larger emissions of this powerful greenhouse gas from marine coastal areas into the atmosphere. In these zones, various electron acceptors such as sulfate, metal oxides, nitrate or oxygen can be utilized. However, the key microbial players and mechanisms of methane oxidation are poorly understood. In this study, we inoculated a bioreactor with methane- and iron-rich sediments from the Bothnian Sea in order to investigate microbial methane and iron cycling under low oxygen concentrations. Using metagenomics, we observed shifts in the microbial community over approximately 2.5 years of bioreactor operation. Marker genes for methane and iron cycling, as well as respiratory and fermentative metabolism, were investigated. Metagenome-assembled genomes representing novel Verrucomicrobia, Bacteroidetes and Krumholzibacteria were recovered and revealed potential for methane oxidation, organic matter degradation, and iron cycling, respectively. This work brings new insights into the identity and metabolic versatility of microorganisms that may be members of such functional guilds in coastal marine sediments and highlights that the methane biofilter in these sediments may be more diverse than previously appreciated. ImportanceDespite the essential role of microorganisms in preventing most methane in the ocean floor to reach the atmosphere, comprehensive knowledge on the identity and the mechanisms employed by these microorganisms is still lacking. This is problematic because such information is needed to understand how the ecosystem functions in the present and how microorganisms may respond to climate change in the future. Here, we enriched and identified novel taxa potentially involved in methane and iron cycling in an oxygen-limited bioreactor inoculated with methane- and iron-rich coastal sediments. Metagenomic analyses provided hypotheses about the mechanisms they may employ, such as the use of oxygen at very low concentrations. The implication of our results is that in more shallow sediments, where oxygen-limited conditions are present, the methane biofilter is potentially composed of novel, metabolically versatile Verrucomicrobia that could contribute to mitigating methane emissions from coastal marine zones.

microbiology↗