Nitrogen-fixing Cyanobacterium Trichodesmium Research Articles

Aluminum-induced changes in the net carbon fixation and carbon decomposition of a nitrogen-fixing cyanobacterium Trichodesmium erythraeum

Aluminum-induced changes in the net carbon fixation and carbon decomposition of a nitrogen-fixing cyanobacterium Trichodesmium erythraeum

Phosphate limitation intensifies negative effects of ocean acidification on globally important nitrogen fixing cyanobacterium

Growth of the prominent nitrogen-fixing cyanobacterium Trichodesmium is often limited by phosphorus availability in the ocean. How nitrogen fixation by phosphorus-limited Trichodesmium may respond to ocean acidification remains poorly understood. Here, we use phosphate-limited chemostat experiments to show that acidification enhanced phosphorus demands and decreased phosphorus-specific nitrogen fixation rates in Trichodesmium. The increased phosphorus requirements were attributed primarily to elevated cellular polyphosphate contents, likely for maintaining cytosolic pH homeostasis in response to acidification. Alongside the accumulation of polyphosphate, decreased NADP(H):NAD(H) ratios and impaired chlorophyll synthesis and energy production were observed under acidified conditions. Consequently, the negative effects of acidification were amplified compared to those demonstrated previously under phosphorus sufficiency. Estimating the potential implications of this finding, using outputs from the Community Earth System Model, predicts that acidification and dissolved inorganic and organic phosphorus stress could synergistically cause an appreciable decrease in global Trichodesmium nitrogen fixation by 2100.

The biogeochemistry and oceanography of the East African Coastal Current

The East African Coastal Current (EACC) is the dominant oceanographic influence along the coastlines of Tanzania and Kenya yet formal descriptions of the biogeochemical characteristics of these waters remain fragmented or poorly defined. Whilst the region remains undersampled, and information for many parameters is limited or even absent, the region is not understudied and complex patterns, due in part to the changing monsoon seasons, can be identified from extant observations. A critical distinction between the neritic waters of the narrow East African continental shelf, which may be more influenced by local tidal currents and terrestrial inputs, and the oligotrophic surface waters of the deeper offshelf region under the influence of the EACC can be drawn, which cautions against the extrapolation of trends or seasonal patterns from limited datasets more widely throughout the region. Permanently N-limited, low NO3−:PO43− surface waters coupled with high (>25 °C) sea surface temperatures are a key feature of the EACC Ecoregion and likely responsible for the presence of a regionally important population of the nitrogen fixing cyanobacterium Trichodesmium, though information on another key requirement, iron, is lacking. Phytoplankton diversity, abundance and the spatiotemporal variability of phytoplankton populations are considered poorly known due to limited sampling efforts. Recent and growing recognition of high coral biodiversity, high reef fish species endemism, of widespread reductions in mangrove forest coverage, and growing anthropogenic pressures on coastal waters suggest that the region deserves greater multidisciplinary study. Efforts to anticipate climate induced changes to these waters, which are expected to impact local fisheries with substantial socioeconomic impacts, would benefit from greater efforts to synthesise existing biogeochemical data, much of which resides within grey literature sources, theses, project reports, remains inaccessible or has been lost. Future biogeochemical and oceanographic observational efforts should simultaneously explore shelf and deeper offshelf waters to determine shelf-to-ocean linkages and the spatiotemporal variability of parameter fields whilst also bridging the gap to research efforts on coral biodiversity, fisheries and marine management activities due to recognised gaps in underlying scientific data to support decision making in these areas.

Functional Genomics and Phylogenetic Evidence Suggest Genus-Wide Cobalamin Production by the Globally Distributed Marine Nitrogen Fixer Trichodesmium.

Only select prokaryotes can biosynthesize vitamin B12 (i.e., cobalamins), but these organic co-enzymes are required by all microbial life and can be vanishingly scarce across extensive ocean biomes. Although global ocean genome data suggest cyanobacteria to be a major euphotic source of cobalamins, recent studies have highlighted that >95% of cyanobacteria can only produce a cobalamin analog, pseudo-B12, due to the absence of the BluB protein that synthesizes the α ligand 5,6-dimethylbenzimidizole (DMB) required to biosynthesize cobalamins. Pseudo-B12 is substantially less bioavailable to eukaryotic algae, as only certain taxa can intracellularly remodel it to one of the cobalamins. Here we present phylogenetic, metagenomic, transcriptomic, proteomic, and chemical analyses providing multiple lines of evidence that the nitrogen-fixing cyanobacterium Trichodesmium transcribes and translates the biosynthetic, cobalamin-requiring BluB enzyme. Phylogenetic evidence suggests that the Trichodesmium DMB biosynthesis gene, bluB, is of ancient origin, which could have aided in its ecological differentiation from other nitrogen-fixing cyanobacteria. Additionally, orthologue analyses reveal two genes encoding iron-dependent B12 biosynthetic enzymes (cbiX and isiB), suggesting that iron availability may be linked not only to new nitrogen supplies from nitrogen fixation, but also to B12 inputs by Trichodesmium. These analyses suggest that Trichodesmium contains the genus-wide genomic potential for a previously unrecognized role as a source of cobalamins, which may prove to considerably impact marine biogeochemical cycles.

Transcriptional Activities of the Microbial Consortium Living with the Marine Nitrogen-Fixing Cyanobacterium Trichodesmium Reveal Potential Roles in Community-Level Nitrogen Cycling.

Trichodesmium is a globally distributed cyanobacterium whose nitrogen-fixing capability fuels primary production in warm oligotrophic oceans. Like many photoautotrophs, Trichodesmium serves as a host to various other microorganisms, yet little is known about how this associated community modulates fluxes of environmentally relevant chemical species into and out of the supraorganismal structure. Here, we utilized metatranscriptomics to examine gene expression activities of microbial communities associated with Trichodesmium erythraeum (strain IMS101) using laboratory-maintained enrichment cultures that have previously been shown to harbor microbial communities similar to those of natural populations. In enrichments maintained under two distinct CO2 concentrations for ∼8 years, the community transcriptional profiles were found to be specific to the treatment, demonstrating a restructuring of overall gene expression had occurred. Some of this restructuring involved significant increases in community respiration-related transcripts under elevated CO2, potentially facilitating the corresponding measured increases in host nitrogen fixation rates. Particularly of note, in both treatments, community transcripts involved in the reduction of nitrate, nitrite, and nitrous oxide were detected, suggesting the associated organisms may play a role in colony-level nitrogen cycling. Lastly, a taxon-specific analysis revealed distinct ecological niches of consistently cooccurring major taxa that may enable, or even encourage, the stable cohabitation of a diverse community within Trichodesmium consortia.IMPORTANCETrichodesmium is a genus of globally distributed, nitrogen-fixing marine cyanobacteria. As a source of new nitrogen in otherwise nitrogen-deficient systems, these organisms help fuel carbon fixation carried out by other more abundant photoautotrophs and thereby have significant roles in global nitrogen and carbon cycling. Members of the Trichodesmium genus tend to form large macroscopic colonies that appear to perpetually host an association of diverse interacting microbes distinct from the surrounding seawater, potentially making the entire assemblage a unique miniature ecosystem. Since its first successful cultivation in the early 1990s, there have been questions about the potential interdependencies between Trichodesmium and its associated microbial community and whether the host's seemingly enigmatic nitrogen fixation schema somehow involved or benefited from its epibionts. Here, we revisit these old questions with new technology and investigate gene expression activities of microbial communities living in association with Trichodesmium.

Biogeographic conservation of the cytosine epigenome in the globally important marine, nitrogen-fixing cyanobacterium Trichodesmium.

Cytosine methylation has been shown to regulate essential cellular processes and impact biological adaptation. Despite its evolutionary importance, only a handful of bacterial, genome-wide cytosine studies have been conducted, with none for marine bacteria. Here, we examine the genome-wide, C5 -Methyl-cytosine (m5C) methylome and its correlation to global transcription in the marine nitrogen-fixing cyanobacterium Trichodesmium. We characterize genome-wide methylation and highlight conserved motifs across three Trichodesmium isolates and two Trichodesmium metagenomes, thereby identifying highly conserved, novel genomic signatures of potential gene regulation in Trichodesmium. Certain gene bodies with the highest methylation levels correlate with lower expression levels. Several methylated motifs were highly conserved across spatiotemporally separated Trichodesmium isolates, thereby elucidating biogeographically conserved methylation potential. These motifs were also highly conserved in Trichodesmium metagenomic samples from natural populations suggesting them to be potential in situ markers of m5C methylation. Using these data, we highlight predicted roles of cytosine methylation in global cellular metabolism providing evidence for a 'core' m5C methylome spanning different ocean regions. These results provide important insights into the m5C methylation landscape and its biogeochemical implications in an important marine N2 -fixer, as well as advancing evolutionary theory examining methylation influences on adaptation.

Stress of life at the ocean’s surface: Latitudinal patterns of UV sunscreens in plankton across the Atlantic

The near-surface layer of the ocean is a habitat in which plankton are subjected to very different stresses to those in deeper layers. These include high turbulence and illumination, allowing increased visibility to predators, and exposure to harmful UV radiation. To provide insights into stress caused by UV, we examined the occurrence of protective UV-absorbing compounds called mycosporine-like amino acids (MAAs) in seston and zooplankton along an Atlantic Meridional Transect (AMT) between 45°S and 50°N. Seston contained most MAAs per unit phytoplankton carbon in the northern Atlantic gyre and equatorial region and this coincided with distribution of the nitrogen fixing cyanobacterium Trichodesmium spp. and increased UV transparency but not irradiance. Asterina-330 was the most abundant MAA in the seston. MAAs were detected in a third of the zooplankton tested and these taxa varied greatly both in the amount and diversity of the MAAs that they contained with copepods in temperate regions containing highest concentration of MAAs. Most commonly found MAAs in zooplankton were palythine and shinorine. Juvenile copepods were found not to contain any MAAs. We determined abundance and richness of zooplankton inhabiting the top 50cm of the ocean. Zooplankton abundance and genera richness was low in the surface waters in contrast to the dome-shaped latitudinal trend in genera richness commonly found from depth-integrated zooplankton sampling. The lack of any measurable MAA compounds in nauplii across the whole transect was concomitant with their severe (3–6-fold) reduction in nauplii densities in the near-surface layer, as compared to the underlying water column. Overall we suggest that the UV stress on life near the surface, particularly in the warmer, oligotrophic and brightly-lit low latitudes, imposes radically different pressures on zooplankton communities compared to the rest of the epipelagic.

Mechanisms of increased Trichodesmium fitness under iron and phosphorus co-limitation in the present and future ocean.

Nitrogen fixation by cyanobacteria supplies critical bioavailable nitrogen to marine ecosystems worldwide; however, field and lab data have demonstrated it to be limited by iron, phosphorus and/or CO2. To address unknown future interactions among these factors, we grew the nitrogen-fixing cyanobacterium Trichodesmium for 1 year under Fe/P co-limitation following 7 years of both low and high CO2 selection. Fe/P co-limited cell lines demonstrated a complex cellular response including increased growth rates, broad proteome restructuring and cell size reductions relative to steady-state growth limited by either Fe or P alone. Fe/P co-limitation increased abundance of a protein containing a conserved domain previously implicated in cell size regulation, suggesting a similar role in Trichodesmium. Increased CO2 further induced nutrient-limited proteome shifts in widespread core metabolisms. Our results thus suggest that N2-fixing microbes may be significantly impacted by interactions between elevated CO2 and nutrient limitation, with broad implications for global biogeochemical cycles in the future ocean.

Missing nitrogen fixation in the Benguela region

Opposing opinions on the importance of nitrogen fixation in the northern Benguela upwelling region provoked us to investigate the magnitude of nitrogen fixation in front of northern Namibia and southern Angola. Measurements of nitrogen fixation rates using the 15N method at 66 stations during seven cruises from 2008 to 2014 showed that, in general, the 15N content in the biomass did not increase after tracer incubation with 15N2, indicating that no nitrogen fixation occurred. Correspondingly, the filamentous nitrogen-fixing cyanobacterium Trichodesmium was almost not present. The abundant picocyanobacteria did obviously not perform nitrogen fixation to a significant degree. The artificial improvement of conditions for nitrogen fixation in mesocosm experiments, including phosphate and iron additions and a warmer temperature, failed to induce nitrogen fixation. A plausible explanation of these findings is a lack of conditioned cells for nitrogen fixation in the Benguela region.

Does eddy‐eddy interaction control surface phytoplankton distribution and carbon export in the North Pacific Subtropical Gyre?

In the North Pacific Subtropical Gyre (NPSG), the regular occurrence of summer phytoplankton blooms contributes to marine ecosystem productivity and the annual carbon export. The mechanisms underlying the formation, maintenance, and decay of these blooms remain largely unknown; nitrogen fixation, episodic vertical mixing of nutrients, and meso‐ (<100 km) and submesoscale (<10 km) physical processes are all hypothesized to contribute to bloom dynamics. In addition, zones of convergence in the ocean's surface layers are known to generate downwelling and/or converging currents that affect plankton distributions. It has been difficult to quantify the importance of these convergence zones in the export flux of particulate organic carbon (POC) in the open ocean. Here we use two high‐resolution ocean transects across a pair of mesoscale eddies in the vicinity of Station ALOHA (22° 45′N, 158° 00′W) to show that horizontal turbulent stirring may have been a dominant control on the spatial distribution of the nitrogen fixing cyanobacteriumTrichodesmium spp. Fast repetition rate fluorometry measurements suggested that this distribution stimulated new primary production; this conclusion was not confirmed by 14C‐based measurements, possibly because of different sampling scales for the two methods. Our observations of particle size distributions along the two transects showed that stretching by the mesoscale eddy field produced submesoscale features that mediated POC export via frontogenetically generated downwelling currents. This study highlights the need to combine high‐resolution biogeochemical and physical data sets to understand the links betweenTrichodesmium spp. surface distribution and POC export in the NPSG at the submesoscale level.

Dust- and mineral-iron utilization by the marine dinitrogen-fixer Trichodesmium

Blooms of the nitrogen-fixing cyanobacterium Trichodesmium, which fuel primary production in tropical and subtropical waters, require large quantities of iron. Laboratory incubations suggest that Trichodesmium accelerates the dissolution of iron oxides and dust, increasing the rate of iron uptake. Trichodesmium, a filamentous dinitrogen-fixing cyanobacterium, forms extensive blooms in nutrient-poor tropical and subtropical ocean waters. These cyano-bacteria contribute significantly to biological fixation of nitrogen from the atmosphere in these waters, and thereby fuel primary production and influence nutrient flow and the cycling of organic and inorganic matter1,2. Trichodesmium blooms require large quantities of iron, which is partly supplied by the influx of wind-blown dust3. However, the processes and mechanisms associated with dust acquisition are poorly understood3,4,5,6. Here, we incubate natural populations and laboratory cultures of Trichodesmium with isotopically labelled iron oxides and desert dust, to determine how these cyanobacteria collect, process and use particulate iron. We show that, like most phytoplankton, Trichodesmium acquires only dissolved iron. However, unlike other studied phytoplankton, Trichodesmium accelerates the rate of iron dissolution from oxides and dust, through as yet unspecified cell-surface processes, and thereby increases cellular iron uptake rates. We show that natural puff (ball-shaped) colonies of Trichodesmium are particularly effective at dissolving dust and oxides, which we attribute to efficient dust trapping in their intricate colony morphology, followed by active shuttling and packaging of the dust within the colony core. We suggest that colony formation in Trichodesmium is an adaptive strategy that enhances iron acquisition from particulate sources such as dust.

A simple, binary classification algorithm for the detection of Trichodesmium spp. within the Great Barrier Reef using MODIS imagery

A binary classification algorithm to detect the presence of high surface concentrations of the nitrogen‐fixing cyanobacterium Trichodesmium spp. was developed for high spatial resolution (250 m) imagery of the Moderate‐resolution Imaging Spectroradiometer (MODIS). Above‐water hyperspectral radiometric measurements of dense Trichodesmium surface aggregations (>10 µg/L Chlorophyll a) showed that the water‐leaving radiance Lw at wavelengths greater than 700 nm were much higher in magnitude (>0.05 W m−2sr−1) relative to the visible wavelengths 400–700 nm (<0.03 W m−2sr−1). The binary classification algorithm is based on three criteria. The first criteria relied on the difference in magnitude between the MODIS normalized water‐leaving radiance (nLw) at the 859 and 678 nm wavebands. The magnitude of the nLw at the 555 and 645 nm wavebands relative to nLw 678 nm waveband formed the second and third criteria, respectively. The classification algorithm was tested on a small subset of 13 MODIS images with corresponding Trichodesmium sea‐truths and yielded an 85% accuracy. Fine‐scale features consistent with dense Trichodesmium surface aggregations, such as eddy swirls and windrows, appear to be well represented with the algorithm results. The algorithm was also found to be robust in the presence of highly reflective, potential confounding effects.

Two flavodoxin genes in Trichodesmium (Oscillatoriales, Cyanophyceae): Remarkable sequence divergence and possible functional diversification

We analyzed flavodoxin gene sequences and transcription patterns in the marine nitrogen-fixing cyanobacterium Trichodesmium Ehrenberg ex Gomont 1892. While a typical cyanobacterial flavodoxin ortholog ( fld1) was identified from cultured (strain IMS101) and environmental Trichodesmium by PCR and Southern blot hybridization, a second flavodoxin ( fld2) was identified in the genome sequence. BLAST and phylogenetic analyses indicated that the two fld genes were highly divergent: fld1 was most closely related to fld common in cyanobacteria, wheras fld2 formed a distinct cluster with a fld so far only found in the unicellular diazotrophic cyanobacteria Cyanothece and Crocosphaera (in which fld2 was the only fld). The fld2 cluster was more closely allied with a fld in non-cyanobacterial diazotrophs such as Azotobacter and Azoarcus than fld1 in other cyanobacteria. This result suggests different evolutionary history of these two genes. Real-Time RT–PCR analysis on iron-replete and iron-deplete Trichodesmium cultures revealed remarkable diel dynamics in transcription of both flds but surprisingly failed to show induction under iron stress. Addition of nitrate to these cultures depressed nifH and fld2 transcription while elevating the transcription of fld1 in iron-stressed cultures. A positive correlation between fld and nifH transcript abundances was found, which was stronger in the case of fld2 than fld1. Our data suggest that these two flavodoxins in Trichodesmium may be functionally diversified and that use of flavodoxin as an iron stress indicator needs to be validated for each organism with consideration of diel dynamics of gene expression.

Genetic diversity of the pelagic harpacticoid copepod Macrosetella gracilis on colonies of the cyanobacterium Trichodesmium spp.

The harpacticoid copepod Macrosetella gracilis uses colonies of the nitrogen-fixing cyanobacterium Trichodesmium spp. as a floating substrate and nursery. This association enables the copepod to lead a pelagic existence. Molecular and morphological data both indicate that M. gracilis is maintained as a single, circumglobal species across the tropical and subtropical Atlantic and Pacific. Mitochondrial DNA sequence data from cytochrome c oxidase subunit I (COI) showed mod- erate to high levels of diversity and limited phylogeographic structure in M. gracilis. Thirty-six differ- ent haplotypes were found among the 149 M. gracilis individuals sequenced; 4 haplotypes were shared between the Atlantic and Pacific. Samples from Japan showed the highest haplotypic and nucleotide diversity levels, suggesting that the Indo-West Pacific may be the center of diversity for M. gracilis. Wide distribution and large population size in M. gracilis may limit divergence through increased gene flow or slowing of the loss of ancestral diversity through lineage sorting. The pelagic existence of M. gracilis has led to less phylogenetic structuring than found in other species of harpacticoid copepods, illustrating the evolutionary significance of specialization on a floating sub- strate in this copepod.

The demise of the marine cyanobacterium, Trichodesmium spp., via an autocatalyzed cell death pathway

We present experimental laboratory evidence and field observations of an autocatalyzed, programmed cell death (PCD) pathway in the nitrogen‐fixing cyanobacterium Trichodesmium spp., which forms massive blooms in the subtropical and tropical oceans. The PCD pathway was induced in response to phosphorus and iron starvation as well as high irradiance and oxidative stress. Transmission electron microscopy revealed morphological degradation of internal components including thylakoids, carboxysomes, and gas vesicles, whereas the plasma membranes remained intact. Physiologically stressed cells displayed significantly elevated endonuclease activity and terminal d‐UTP nick‐end labeling. Nucleic acid degradation was concordant with increased immunoreactivity to human caspase‐3 polyclonal antisera and enhanced cleavage of a caspase‐specific substrate, DEVD. Caspase activity was positively correlated with mortality and was inhibited by the irreversible caspase inhibitor Z‐VAD‐FMK. A search of the Trichodesmium erythraeum genome identified several protein sequences containing a conserved caspase domain structure, including the histidine‐ and cysteine‐containing catalytic diad found in true caspases, paracaspases, and metacaspases. Induction of PCD by caspase‐like proteases in a bacterial photoautotroph with an ancient evolutionary history requires a reassessment about the origins and roles of cell death cascades. This process is a previously unappriciated mortality mechanism that can lead to the termination of natural Trichodesmium blooms and that can influence the fluxes of organic matter in the ocean.

Primary production by phytoplankton along the Kenyan coast during the SE monsoon and November intermonsoon 1992, and the occurrence of Trichodesmium

Phytoplanktonic primary production was measured during the SE monsoon in June–July and during the intermonsoon period in November–December 1992. Primary production was highest on the northernmost transect during the SE monsoon, whereas during the intermonsoon it was highest on the southernmost transect. In general primary production was higher during the intermonsoon, and highest productivity was measured along the southern coast of Kenya. The more stable hydrodynamical conditions during the intermonsoon period promoted the occurrence of the nitrogen-fixing cyanobacterium Trichodesmium, primarily at the shallower stations. Nitrogen fixation assays suggested that this cyanobacterium was responsible for most of the new production. Comparison between net primary productivity, bacterial productivity and benthic respiration suggests that rates of primary production should be higher than measured, implying that primary production can be as high as that in tropical upwelling systems, despite the fact that a regular and well-developed upwelling period does not always seem to occur.

Unique modification of adenine in genomic DNA of the marine cyanobacterium Trichodesmium sp. strain NIBB 1067.

The genomic DNA of the marine nonheterocystous nitrogen-fixing cyanobacterium Trichodesmium sp. strain NIBB 1067 was found to be highly resistant to DNA restriction endonucleases. The DNA was digested extensively by the restriction enzyme DpnI, which requires adenine methylation for activity. The DNA composition, determined by high-performance liquid chromatography (HPLC), was found to be 69% AT. Surprisingly, it was found that a modified adenine which was not methylated at the usual N6 position was present and made up 4.7 mol% of the nucleosides in Trichodesmium DNA (15 mol% of deoxyadenosine). In order for adenine residues to be modified at this many positions, there must be many modifying enzymes or at least one of the modifying enzymes must have a degenerate recognition site. The reason(s) for this extensive methylation has not yet been determined but may have implications for the ecological success of this microorganism in nature.