Biology subjects

Lucker, S.

Publications and source records attributed to Lucker, S..

3 recordsLinked to original sources

bioRxiv2017

Linking nitrogen load to the structure and function of wetland soil and rhizosphere microbial communities

Wetland ecosystems are important reservoirs of biodiversity and significantly contribute to emissions of the greenhouse gases CO2, NO2 and CH4. High anthropogenic nitrogen (N) inputs from agriculture and fossil fuel combustion have been recognized as a severe threat to biodiversity and ecosystem functioning such as control of greenhouse gas emissions. Therefore it is important to understand how increased N input into pristine wetlands affects the composition and activity of micro-organisms, especially in interaction with dominant wetland plants. In a series of incubations analyzed over 90 days, we disentangle the effects of N fertilization on the microbial community in bulk soil and the rhizosphere of Juncus acutiflorus, a common and abundant graminoid wetland plant. We observed an increase in greenhouse gas emissions when N is increased in incubations with J. acutiflorus, changing the system from a greenhouse gas sink to a source. Using 16S rRNA amplicon sequencing and metagenomics, we determined that the bacterial orders Opitutales, Subgroup-6 Acidobacteria and Sphingobacteriales significantly responded to high N availability and we hypothesize that these groups are contributing to the increased greenhouse gas emissions. These results indicated that increased N input leads to shifts in microbial activity within the rhizosphere, severely altering N cycling dynamics. Our study provides a framework for connecting environmental conditions of wetland bulk and rhizosphere soil to the structure and metabolic output of microbial communities.

microbiology↗

bioRxiv2017

Nitrogen-Fixing Populations Of Planctomycetes And Proteobacteria Are Abundant In The Surface Ocean

Nitrogen fixation in the surface ocean impacts the global climate by regulating the microbial primary productivity and the sequestration of carbon through the biological pump. Cyanobacterial populations have long been thought to represent the main suppliers of the bio-available nitrogen in this habitat. However, recent molecular surveys of nitrogenase reductase gene revealed the existence of rare non-cyanobacterial populations that can also fix nitrogen. Here, we characterize for the first time the genomic content of some of these heterotrophic bacterial diazotrophs (HBDs) inhabiting the open surface ocean waters. They represent new lineages within Planctomycetes and Proteobacteria, a phylum never linked to nitrogen fixation prior to this study. HBDs were surprisingly abundant in the Pacific Ocean and the Atlantic Ocean northwest, conflicting with decades of PCR surveys. The abundance and widespread occurrence of non-cyanobacterial diazotrophs in the surface ocean emphasizes the need to re-evaluate their role in the nitrogen cycle and primary productivity.

microbiology↗

bioRxiv2016

AmoA-targeted polymerase chain reaction primers for the specific detection and quantification of comammox Nitrospira in the environment

Nitrification, the oxidation of ammonia via nitrite to nitrate, has always been considered to be catalyzed by the concerted activity of ammonia and nitrite-oxidizing microorganisms. Only recently, complete ammonia oxidizers ( comammox), which oxidize ammonia to nitrate on their own, were identified in the bacterial genus Nitrospira, previously assumed to contain only canonical nitrite oxidizers. Nitrospira are widespread in nature, but for assessments of the distribution and functional importance of comammox Nitrospira in ecosystems, cultivation-independent tools to distinguish comammox from strictly nitrite-oxidizing Nitrospira are required. Here we developed new PCR primer sets that specifically target the amoA genes coding for subunit A of the distinct ammonia monooxygenase of comammox Nitrospira. While existing primers capture only a fraction of the known comammox amoA diversity, the new primer sets cover as much as 95% of the comammox amoA clade A and 92% of the clade B sequences in a reference database containing 326 comammox amoA genes with sequence information at the primer binding sites. Application of the primers to 13 samples from engineered systems (a groundwater well, drinking water treatment and wastewater treatment plants) and other habitats (rice paddy and forest soils, rice rhizosphere, brackish lake sediment and freshwater biofilm) detected comammox Nitrospira in all samples and revealed a considerable diversity of comammox in most habitats. Excellent primer specificity for comammox amoA was achieved by avoiding the use of highly degenerate primer preparations and by using equimolar mixtures of oligonucleotides that match existing comammox amoA genes. Quantitative PCR with these equimolar primer mixtures was highly sensitive and specific, and enabled the efficient quantification of clade A and clade B comammox amoA gene copy numbers in environmental samples. The measured relative abundances of comammox Nitrospira, compared to canonical ammonia oxidizers, were highly variable across environments. The new comammox amoA-targeted primers will enable more encompassing studies of nitrifying microorganisms in diverse ecosystems.

microbiology↗