Hutchins
David A.
Hutchins
David A.
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PreprintComment on “The complex effects of ocean acidification on the prominent N2-fixing cyanobacterium Trichodesmium”( 2017-08) Hutchins, David A. ; Fu, Feixue ; Walworth, Nathan G. ; Lee, Michael D. ; Saito, Mak A. ; Webb, Eric A.Hong et al. (Reports, 5 May 2017, p. 527) suggested that previous studies of the biogeochemically significant marine cyanobacterium Trichodesmium showing increased growth and nitrogen fixation at projected future high CO2 levels suffered from ammonia or copper toxicity. They reported that these rates instead decrease at high CO2 when contamination is alleviated. We present and discuss results of multiple published studies refuting this toxicity hypothesis.
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ArticleFunctional genomics and phylogenetic evidence suggest genus-wide cobalamin production by the globally distributed marine nitrogen fixer Trichodesmium(Frontiers Media, 2018-02-13) Walworth, Nathan G. ; Lee, Michael D. ; Suffridge, Christopher ; Qu, Pingping ; Fu, Fei-Xue ; Saito, Mak A. ; Webb, Eric A. ; Sañudo-Wilhelmy, Sergio A. ; Hutchins, David A.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.
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ArticleMechanisms of increased Trichodesmium fitness under iron and phosphorus co-limitation in the present and future ocean(Nature Publishing Group, 2016-06-27) Walworth, Nathan G. ; Fu, Fei-Xue ; Webb, Eric A. ; Saito, Mak A. ; Moran, Dawn M. ; Mcllvin, Matthew R. ; Lee, Michael D. ; Hutchins, David A.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.
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ArticleImportance of mobile genetic element immunity in numerically abundant Trichodesmium clades(Springer, 2023-02-23) Webb, Eric A. ; Held, Noelle A. ; Zhao, Yiming ; Graham, Elaina D. ; Conover, Asa E. ; Semones, Jake ; Lee, Michael D. ; Feng, Yuanyuan ; Fu, Fei-Xue ; Saito, Mak A. ; Hutchins, David A.The colony-forming cyanobacteria Trichodesmium spp. are considered one of the most important nitrogen-fixing genera in the warm, low nutrient ocean. Despite this central biogeochemical role, many questions about their evolution, physiology, and trophic interactions remain unanswered. To address these questions, we describe Trichodesmium pangenomic potential via significantly improved genomic assemblies from two isolates and 15 new >50% complete Trichodesmium metagenome-assembled genomes from hand-picked, Trichodesmium colonies spanning the Atlantic Ocean. Phylogenomics identified ~four Nfixing clades of Trichodesmium across the transect, with T. thiebautii dominating the colony-specific reads. Pangenomic analyses showed that all T. thiebautii MAGs are enriched in COG defense mechanisms and encode a vertically inherited Type III-B Clustered Regularly Interspaced Short Palindromic Repeats and associated protein-based immunity system (CRISPR-Cas). Surprisingly, this CRISPR-Cas system was absent in all T. erythraeum genomes, vertically inherited by T. thiebautii, and correlated with increased signatures of horizontal gene transfer. Additionally, the system was expressed in metaproteomic and transcriptomic datasets and CRISPR spacer sequences with 100% identical hits to field-assembled, putative phage genome fragments were identified. While the currently CO-limited T. erythraeum is expected to be a 'winner' of anthropogenic climate change, their genomic dearth of known phage resistance mechanisms, compared to T. thiebautii, could put this outcome in question. Thus, the clear demarcation of T. thiebautii maintaining CRISPR-Cas systems, while T. erythraeum does not, identifies Trichodesmium as an ecologically important CRISPR-Cas model system, and highlights the need for more research on phage-Trichodesmium interactions.