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.
Nitrogen (Formula: see text) fixation by heterotrophic bacteria associated with sinking particles contributes to marine N cycling, but a mechanistic understanding of its regulation and significance ...are not available. Here we develop a mathematical model for unicellular heterotrophic bacteria growing on sinking marine particles. These bacteria can fix Formula: see text under suitable environmental conditions. We find that the interactive effects of polysaccharide and polypeptide concentrations, sinking speed of particles, and surrounding Formula: see text and Formula: see text concentrations determine the Formula: see text fixation rate inside particles. Formula: see text fixation inside sinking particles is mainly fueled by Formula: see text respiration rather than Formula: see text respiration. Our model suggests that anaerobic processes, including heterotrophic Formula: see text fixation, can take place in anoxic microenvironments inside sinking particles even in fully oxygenated marine waters. The modelled Formula: see text fixation rates are similar to bulk rates measured in the aphotic ocean, and our study consequently suggests that particle-associated heterotrophic Formula: see text fixation contributes significantly to oceanic Formula: see text fixation.
Nitrogen fixation provides bioavailable nitrogen, supporting global ecosystems and influencing global cycles of other elements. It provides an additional source of nitrogen to organisms at a cost of ...lower growth efficiency, largely due to respiratory control of intra-cellular oxygen. Nitrogen-fixing bacteria can, however, utilize both dinitrogen gas and fixed nitrogen, decreasing energetic costs. Here we present an idealized metabolic model of the heterotrophic nitrogen fixer Azotobacter vinelandii which, constrained by laboratory data, provides quantitative predictions for conditions under which the organism uses either ammonium or nitrogen fixation, or both, as a function of the relative supply rates of carbohydrate, fixed nitrogen as well as the ambient oxygen concentration. The model reveals that the organism respires carbohydrate in excess of energetic requirements even when nitrogen fixation is inhibited and respiratory protection is not essential. The use of multiple nitrogen source expands the potential niche and range for nitrogen fixation. The model provides a quantitative framework which can be employed in ecosystem and biogeochemistry models.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Variation in traits causes bacterial populations to respond in contrasting ways to environmental drivers. Learning about this will help us understand the ecology of individual populations in complex ...ecosystems. We used 454 pyrosequencing of the hypervariable region V6 of the 16S rRNA gene to study seasonal dynamics in Baltic Sea bacterioplankton communities, and link community and population changes to biological and chemical factors. Surface samples were collected from May to October 2003 and in May 2004 at the Landsort Deep in the central Baltic Sea Proper. The analysis rendered, on average, 20 200 sequence reads for each of the eight samples analyzed, providing the first detailed description of Baltic Sea bacterial communities. Community composition varied dramatically over time, supporting the idea of strong temporal shifts in bacterioplankton assemblages, and clustered according to season (including two May samples from consecutive years), suggesting repeatable seasonal succession. Overall, community change was most highly correlated with change in phosphorus concentration and temperature. Individual bacterial populations were also identified that tightly co-varied with different Cyanobacteria populations. Comparing the abundance profiles of operational taxonomic units at different phylogenetic distances revealed a weak but significant negative correlation between abundance profile similarity and genetic distance, potentially reflecting habitat filtering of evolutionarily conserved functional traits in the studied bacterioplankton.
Nitrogen‐fixing microorganisms (diazotrophs) provide biologically available nitrogen to plankton communities and thereby greatly influence the productivity in many marine regions. Various ...cyanobacterial groups have traditionally been considered the major oceanic diazotrophs, but later noncyanobacterial and presumably heterotrophic diazotrophs were also found to be widespread and potentially important in nitrogen fixation. However, the distribution and activity of different diazotroph groups is still poorly constrained for most oceanic ecosystems. Here we examined diazotroph community structure and activity along a 7500 km south‐north transect between the central equatorial Pacific and the Bering Sea. Nitrogen fixation contributed up to 84% of new production in the upper waters of the subtropical gyre, where the diazotroph community included the gammaproteobacterium γ‐24774A11 and highly active cyanobacterial phylotypes (>50% of total nifH transcript abundance). Nitrogen fixation was sometimes detectable down to 150 m depth and extended horizontally to the edge of the gyre at around 35°N. Nitrogen fixation was even detected far north on the Bering Sea shelf. In the Alaskan Coastal Waters on the Bering Sea shelf, low nitrate together with high dissolved iron concentrations seemed to foster diazotroph growth, including a prominent role of UCYN‐A2, which was abundant near the surface (1.2×105 nifH gene copies L−1). Our study provides evidence for nitrogen fixation in the Bering Sea and suggests a clear contrast in the composition of diazotrophs between the tropical/subtropical gyre and the separate waters in the cold northern regions of the North Pacific.
Key Points
N2 fixation in the North Pacific occurred not only in the tropics and subtropics but also in the subarctic Bering Sea
Cyanobacterial nifH gene expression exceeds that of noncyanobacterial diazotrophs on a diurnal basis in the tropics and subtropics
UCYN‐A2 was the dominant diazotroph in the cold, nitrate‐depleted, and iron‐rich Bering Sea
The Arctic Ocean is the smallest ocean on Earth, yet estimated to play a substantial role as a global carbon sink. As climate change is rapidly changing fundamental components of the Arctic, it is of ...local and global importance to understand and predict consequences for its carbon dynamics. Primary production in the Arctic Ocean is often nitrogen-limited, and this is predicted to increase in some regions. It is therefore of critical interest that biological nitrogen fixation, a process where some bacteria and archaea termed diazotrophs convert nitrogen gas to bioavailable ammonia, has now been detected in the Arctic Ocean. Several studies report diverse and active diazotrophs on various temporal and spatial scales across the Arctic Ocean. Their ecology and biogeochemical impact remain poorly known, and nitrogen fixation is so far absent from models of primary production in the Arctic Ocean. The composition of the diazotroph community appears distinct from other oceans - challenging paradigms of function and regulation of nitrogen fixation. There is evidence of both symbiotic cyanobacterial nitrogen fixation and heterotrophic diazotrophy, but large regions are not yet sampled, and the sparse quantitative data hamper conclusive insights. Hence, it remains to be determined to what extent nitrogen fixation represents a hitherto overlooked source of new nitrogen to consider when predicting future productivity of the Arctic Ocean. Here, we discuss current knowledge on diazotroph distribution, composition, and activity in pelagic and sea ice-associated environments of the Arctic Ocean. Based on this, we identify gaps and outline pertinent research questions in the context of a climate change-influenced Arctic Ocean - with the aim of guiding and encouraging future research on nitrogen fixation in this region.
Traditionally, cyanobacterial activity in oceanic photic layers was considered responsible for the marine pelagic dinitrogen (N
) fixation. Other potentially N
-fixing bacteria and archaea have also ...been detected in the pelagic water column, however, the activity and importance of these non-cyanobacterial diazotrophs (NCDs) remain poorly constrained. In this perspective we summarize the N
fixation rates from recently published studies on photic and aphotic layers that have been attributed to NCD activity via parallel molecular measurements, and discuss the status, challenges, and data gaps in estimating non-cyanobacterial N
fixation NCNF in the ocean. Rates attributed to NCNF have generally been near the detection limit thus far (<1 nmol N L
d
). Yet, if considering the large volume of the dark ocean, even low rates of NCNF could make a significant contribution to the new nitrogen input to the ocean. The synthesis here shows that
transcription data for NCDs have been reported in only a few studies where N
fixation rates were detected in the absence of diazotrophic cyanobacteria. In addition, high apparent diversity and regional variability in the NCDs complicate investigations of these communities. Future studies should focus on further investigating impacts of environmental drivers including oxygen, dissolved organic matter, and dissolved inorganic nitrogen on NCNF. Describing the ecology of NCDs and accurately measuring NCNF rates, are critical for a future evaluation of the contribution of NCNF to the marine nitrogen budget.
An initial modeling approach was applied to analyze how a single, nonmotile, free-living, heterotrophic bacterial cell may optimize the deployment of its extracellular enzymes. Free-living cells live ...in a dilute and complex substrate field, and to gain enough substrate, their extracellular enzymes must be utilized efficiently. The model revealed that surface-attached and free enzymes generate unique enzyme and substrate fields, and each deployment strategy has distinctive advantages. For a solitary cell, surface-attached enzymes are suggested to be the most cost-efficient strategy. This strategy entails potential substrates being reduced to very low concentrations. Free enzymes, on the other hand, generate a radically different substrate field, which suggests significant benefits for the strategy if free cells engage in social foraging or experience high substrate concentrations. Swimming has a slight positive effect for the attached-enzyme strategy, while the effect is negative for the free-enzyme strategy. The results of this study suggest that specific dissolved organic compounds in the ocean likely persist below a threshold concentration impervious to biological utilization. This could help explain the persistence and apparent refractory state of oceanic dissolved organic matter (DOM). Microbial extracellular enzyme strategies, therefore, have important implications for larger-scale processes, such as shaping the role of DOM in ocean carbon sequestration.
Viruses are fundamental to ecosystems ranging from oceans to humans, yet our ability to study them is bottlenecked by the lack of ecologically relevant isolates, resulting in “unknowns” dominating ...culture-independent surveys. Here we present genomes from 31 phages infecting multiple strains of the aquatic bacterium Cellulophaga baltica (Bacteroidetes) to provide data for an underrepresented and environmentally abundant bacterial lineage. Comparative genomics delineated 12 phage groups that (i) each represent a new genus, and (ii) represent one novel and four well-known viral families. This diversity contrasts the few well-studied marine phage systems, but parallels the diversity of phages infecting human-associated bacteria. Although all 12 Cellulophaga phages represent new genera, the podoviruses and icosahedral, nontailed ssDNA phages were exceptional, with genomes up to twice as large as those previously observed for each phage type. Structural novelty was also substantial, requiring experimental phage proteomics to identify 83% of the structural proteins. The presence of uncommon nucleotide metabolism genes in four genera likely underscores the importance of scavenging nutrient-rich molecules as previously seen for phages in marine environments. Metagenomic recruitment analyses suggest that these particular Cellulophaga phages are rare and may represent a first glimpse into the phage side of the rare biosphere. However, these analyses also revealed that these phage genera are widespread, occurring in 94% of 137 investigated metagenomes. Together, this diverse and novel collection of phages identifies a small but ubiquitous fraction of unknown marine viral diversity and provides numerous environmentally relevant phage–host systems for experimental hypothesis testing.
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