Simultaneous quantification of active carbon- and nitrogen-fixing communities and estimation of fixation rates using fluorescence in situ hybridization and flow cytometry

Non-cyanobacterial diazotrophs: global diversity, distribution, ecophysiology, and activity in marine waters

Biological dinitrogen (N2) fixation supplies nitrogen to the oceans, supporting primary productivity, and is carried out by some bacteria and archaea referred to as diazotrophs. Cyanobacteria are conventionally considered to be the major contributors to marine N2 fixation, but non-cyanobacterial diazotrophs (NCDs) have been shown to be distributed throughout ocean ecosystems. However, the biogeochemical significance of marine NCDs has not been demonstrated. This review synthesizes multiple datasets, drawing from cultivation-independent molecular techniques and data from extensive oceanic expeditions, to provide a comprehensive view into the diversity, biogeography, ecophysiology, and activity of marine NCDs. A NCD nifH gene catalog was compiled containing sequences from both PCR-based and PCR-free methods, identifying taxa for future studies. NCD abundances from a novel database of NCD nifH-based abundances were colocalized with environmental data, unveiling distinct distributions and environmental drivers of individual taxa. Mechanisms that NCDs may use to fuel and regulate N2 fixation in response to oxygen and fixed nitrogen availability are discussed, based on a metabolic analysis of recently available Tara Oceans expedition data. The integration of multiple datasets provides a new perspective that enhances understanding of the biology, ecology, and biogeography of marine NCDs and provides tools and directions for future research.

Analysis of nifH-RNA reveals phylotypes related to Geobacter and Cyanobacteria as important functional components of the N2 -fixing community depending on depth and agricultural use of soil

In this survey, a total of 80 787 reads and 28 171 unique NifH protein sequences were retrieved from soil RNA. This dataset extends our knowledge about the structure and diversity of the functional diazotrophic communities in agricultural soils from Argentinean Pampas. Operational taxonomic unit (OTU)‐based analyses showed that nifH phylotypes related to Geobacter and Anaeromyxobacter (44.8%), Rhizobiales (29%), Cyanobacteria (16.7%), and Verrucomicrobiales (8%) are key microbial components of N₂ fixation in soils associated with no‐till management and soil depth. In addition, quantification of nifH gene copies related to Geobacter and Cyanobacteria revealed that these groups are abundant in soils under maize–soybean rotation and soybean monoculture, respectively. The correlation of physicochemical soil parameters with the diazotrophic diversity and composition showed that soil stability and organic carbon might contribute to the functional signatures of particular nifH phylotypes in fields under no‐till management. Because crop production relies on soil‐borne microorganism's activities, such as free N₂ fixation, the information provided by our study on the diazotrophic population dynamics, associated with the edaphic properties and land‐use practices, represents a major contribution to gain insight into soil biology, in which functionally active components are identified.

Fluorescence in situ hybridization of Microcystis strains producing microcystin using specific mRNA probes

Cyanobacteria are ubiquitous micro-organisms that can produce toxic compounds, the cyanotoxins. The monitoring of such producers in the environment is of prime importance for human health. An attractive technology for such monitoring is fluorescence in situ hybridization (FISH), which allows the detection and enumeration of environmental micro-organisms. We present here the application of tyramide signal amplification fluorescence in situ hybridization (TSA-FISH) to the detection of microcystin-producing Microcystis strains. We used a 16S rRNA-specific probe, MICR3, to specifically label and observe by epifluorescence microscopy Microcystis aeruginosa strains. Using confocal laser scanning microscopy and a specific probe, MCYA, targeting the mcyA mRNA we have labelled M. aeruginosa PCC 7806, which produces microcystins. Microcystis aeruginosa PCC 7005 which does not produce microcystins is not labelled by this probe. Furthermore, we show here that this specific mRNA labelling in M. aeruginosa PCC 7806 is enhanced in cells illuminated for 1 h just after a dark period of cultivation of 24 h, conditions in which the mcyA gene is up regulated. The data presented here might be applicable to the monitoring of toxic Microcystis strains in the environment.

SIGNIFICANCE AND IMPACT OF THE STUDY

Cyanobacteria producing toxic compounds (cyanotoxins) are present in the environment and in water bodies. Their presence poses a threat on human and animal health. It is thus important to detect, identify and enumerate these toxic Cyanobacteria. Using tyramide signal amplification fluorescence in situ hybridization (TSA-FISH) and specific probes, with confocal laser scanning microscopy, we have specifically detected Microcystis strains producing microcystin toxins. The data presented here might be applied to the monitoring of water bodies at early stages and all along the formation of Microcystis blooms.

Marine Non-Cyanobacterial Diazotrophs: Moving beyond Molecular Detection

The nitrogen input through biological N₂ fixation is essential for life in vast areas of the global ocean. The belief is that cyanobacteria are the only relevant N₂-fixing (diazotrophic) organisms. It has, however, now become evident that non-cyanobacterial diazotrophs, bacteria and archaea with ecologies fundamentally distinct from those of cyanobacteria, are widespread and occasionally fix N₂ at significant rates. The documentation of a globally relevant nitrogen input from these diazotrophs would constitute a new paradigm for research on oceanic nitrogen cycling. Here we highlight the need for combining rate measurements and molecular analyses of field samples with cultivation studies in order to clarify the ecology of non-cyanobacteria and their contribution to marine N₂ fixation on local and global scales.