Biology subjects

Hutchins, D. A.

Publications and source records attributed to Hutchins, D. A..

8 recordsLinked to original sources

bioRxiv2023

Responses of keystone phytoplankton groups to olivine dissolution products and implications for carbon dioxide removal via ocean alkalinity enhancement

Anthropogenic greenhouse gas emissions are leading to global temperature increases, ocean acidification, and significant ecosystem impacts. Given current emissions trajectories, the IPCC reports indicate that rapid abatement of CO2 emissions and development of carbon dioxide removal (CDR) strategies are needed to address legacy and difficult to abate emissions sources. These CDR methods must efficiently and safely sequester gigatons of atmospheric CO2. Coastal Enhanced Weathering (CEW) via the addition of the common mineral olivine to coastal waters is one promising approach to enhance ocean alkalinity for large-scale CDR. As olivine weathers, it releases several biologically active dissolution products, including alkalinity, trace metals, and the nutrient silicate. Released trace metals can serve as micronutrients but may also be toxic at high concentrations to marine biota including phytoplankton that lie at the base of marine food webs. We grew six species representing several globally important phytoplankton species under elevated concentrations of olivine dissolution products via a synthetic olivine leachate (OL) based on olivine elemental composition. We monitored their physiological and biogeochemical responses, which allowed us to determine physiological impacts and thresholds at elevated olivine leachate concentrations, in addition to individual effects of specific constituents. We found both positive and neutral responses but no evident toxic effects for two silicifying diatoms, a calcifying coccolithophore, and three cyanobacteria. In both single and competitive co-cultures, silicifiers and calcifiers benefited from olivine dissolution products like iron and silicate or enhanced alkalinity, respectively. The non-N2-fixing picocyanobacterium could use synthetic olivine-derived iron for growth, while N2-fixing cyanobacteria could not. However, other trace metals like nickel and cobalt supported cyanobacterial growth across both groups. Growth benefits to phytoplankton groups in situ will depend on species-specific responses and ambient concentrations of other required nutrients. Results suggest olivine dissolution products appear unlikely to cause negative physiological effects for any of the phytoplankton examined, even at high concentrations, and may support growth of particular taxa under some conditions. Future studies can shed light on long-term eco-evolutionary responses to olivine exposure and on the potential effects that marine microbes may in turn have on olivine dissolution rates and regional biogeochemistry.

microbiology↗

bioRxiv2022

Importance of Mobile Genetic Element Immunity in Numerically Abundant Trichodesmium Clades

The colony-forming cyanobacteria Trichodesmium spp. are considered one of the most important nitrogen-fixing genera in the warm, low nutrient, open ocean. Despite this central biogeochemical role, many questions about their evolution, physiology, and trophic interactions remain unanswered. To address these questions, we describe the genetic potential of the genus via significantly improved genomic assemblies of strains Trichodesmium thiebautii H94, Trichodesmium erythraeum 2175, and 17 new Trichodesmium metagenome-assembled genomes (MAGs, >50% complete) from hand-picked, Trichodesmium colonies spanning the Atlantic Ocean. Phylogenomics identified [~]four N2 fixing 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 defense mechanisms and encode a vertically inherited Type III-B Clustered Regularly Interspaced Short Palindromic Repeats and associated protein-based immunity system (CRISPR-Cas hereafter). Surprisingly, this CRISPR-Cas system was absent in all T. erythraeum genomes and MAGs, vertically inherited by T. thiebautii, and correlated with increased signatures of horizontal gene transfer. Multiple lines of evidence indicate that the CRISPR-Cas system is functional in situ: 1. Trichodesmium CRISPR spacer sequences with 100% identical hits to field-assembled, putative phage genome fragments were identified, 2. High Trichodesmium spacer sequence variability indicating rapid adaptation, and 3. metaproteomic and transcriptomic expression analyses detecting the CRISPR-Cas system components in Trichodesmium colonies from the Atlantic and Pacific Oceans. These data suggest that phage or mobile genetic element immunity in T. thiebautii could contribute to their success, gene diversity, and numerical dominance over T. erythraeum in the oceans, thus warranting further Trichodesmium virome investigations. Significance statementOur work identifies CRISPR-Cas immunity as a phylogenetically distinct, environmentally expressed factor in the speciation of closely related N2-fixing Trichodesmium clades. These findings suggest that differential phage predation and resistance could be a previously overlooked selective pressure in the genus, potentially leading to the current numerical dominance of T. thiebautii over T. erythraeum in the oceans. Furthermore, while the currently CO2-limited T. erythraeum is expected to be a winner of anthropogenic climate change, their predicted higher phage sensitivity than T. thiebautii could challenge this outcome.

microbiology↗

bioRxiv2021

Why Environmental Biomarkers Work: Transcriptome-Proteome Correlations and Modeling of Multi-Stressor Experiments in the Marine Bacterium Trichodesmium

Ocean microbial communities are important contributors to the global biogeochemical reactions that sustain life on Earth. The factors controlling these communities are being increasingly explored through the use of metatranscriptomic and metaproteomic environmental biomarkers, despite ongoing uncertainty about the coherence between RNA and protein signals. Using published proteomes and transcriptomes from the abundant colony-forming cyanobacterium Trichodesmium (strain T. erythraeum IMS101) grown under varying Fe and/or P limitation and/or co-limitation in low and high CO2, we observed robust correlations of stress induced proteins and RNAs (i.e., those involved in transport and homeostasis) that can yield useful information on nutrient status under low and/or high CO2. Conversely, transcriptional and translational correlations of many other central metabolism pathways exhibit broad discordance. A cellular RNA and protein production/degradation model demonstrates how biomolecules with small initial inventories, such as environmentally responsive proteins, can achieve large increases in fold-change units, as opposed to those with higher basal expression and inventory such as metabolic systems. Microbial cells, due to their close proximity to the environment, tend to show large adaptive responses to environmental stimuli in both RNA and protein that result in transcript-protein correlations. These observations and model results demonstrate a multi-omic coherence for environmental biomarkers and provide the underlying mechanism for those observations, supporting the promise for global application in detecting responses to environmental stimuli in a changing ocean.

microbiology↗

bioRxiv2021

Alphaproteobacteria facilitate Trichodesmium community trimethylamine utilization

In the surface waters of the warm oligotrophic ocean, filaments and aggregated colonies of the nitrogen (N)-fixing cyanobacterium Trichodesmium create microscale nutrient-rich oases. These hotspots fuel primary productivity and harbor a diverse consortium of heterotrophs. Interactions with associated microbiota can affect the physiology of Trichodesmium, often in ways that have been predicted to support its growth. Recently, it was found that trimethylamine (TMA), a globally-abundant organic N compound, inhibits N2 fixation in cultures of Trichodesmium without impairing growth rate, suggesting that Trichodesmium receives nitrogen from TMA. In this study, 15N-TMA DNA stable isotope probing (SIP) of a Trichodesmium enrichment was employed to further investigate TMA metabolism and determine if TMA-N is incorporated directly or secondarily via cross-feeding facilitated by microbial associates. Herein we identify two members of the marine Roseobacter clade (MRC) of Alphaproteobacteria as the likely metabolizers of TMA and provide genomic evidence that they converted TMA into a more readily available form of N, e.g., NH4+, which was subsequently used by Trichodesmium and the rest of the community. The results implicate microbiome-mediated carbon (C) and N transformations in modulating N2 fixation, and thus highlight the involvement of host-associated heterotrophs in global biogeochemical cycling.

microbiology↗

bioRxiv2020

Mechanisms and heterogeneity of mineral use by natural colonies of the cyanobacterium Trichodesmium

The keystone marine nitrogen fixer Trichodesmium thrives in high dust environments, and while experimental observations suggest that Trichodesmium colonies can access the essential nutrient iron from dust particles, it is not known the extent to which this occurs in the field. Here we demonstrate that Trichodesmium colonies actively process mineral particles in nature with direct molecular impacts. Microscopy and synchrotron-based imaging demonstrated heterogeneous associations with particles consistent with iron oxide and iron silicate minerals. Metaproteomic analysis of individual colonies revealed enrichment of biogeochemically-relevant proteins including photosynthesis proteins and metalloproteins containing iron, nickel, copper and zinc when particles were present. The iron-storage protein ferritin was particularly enriched implying accumulation of particle-derived iron, and multiple iron acquisition pathways including Fe(II), Fe(III), and Fe-siderophore transporters were engaged, including evidence of superoxide-driven particle dissolution. While the particles clearly provided iron, there was also evidence that the concentrated metals had toxic effects. The molecular mechanisms allowing Trichodesmium to interact with particulate minerals are fundamental to its success and global impact on nitrogen biogeochemistry, and may contribute to the leaching of particulate trace metals with implications for global iron and carbon cycling.

ecology↗

bioRxiv2020

Irradiance modulates thermal niche in a previously undescribed low-light and cold-adapted nano-diatom

Diatoms have well-recognized roles in fixing and exporting carbon and supplying energy to marine ecosystems, but only recently have we begun to explore the diversity and importance of nano- and pico-diatoms. Here we describe a small (~5 m) diatom from the genus Chaetoceros Isolated from a wintertime temperate estuary (2{degrees} C, Narragansett Bay, RI), with a unique obligate specialization for low-light environments (< 120 mol photons m-2 sec-1). This diatom exhibits a striking interaction between irradiance and thermal responses whereby as temperatures increase, so does its susceptibility to light stress. Historical 18S rRNA amplicon data from our study site show this isolate was abundant throughout a six-year period, and its presence strongly correlates with winter and early spring months when light and temperature are low. Two ASVs matching this isolate had a circumpolar distribution in Tara Polar Ocean Circle samples, indicating its unusual light and temperature requirements are adaptations to life in a cold, dark environment. We expect this isolates low light, psychrophilic niche to shrink as future warming-induced stratification increases both light and temperature levels experienced by high latitude marine phytoplankton.

microbiology↗

bioRxiv2020

Molecular underpinnings and biogeochemical consequences of enhanced diatom growth in a warming Southern Ocean

The Southern Ocean (SO) harbours some of the most intense phytoplankton blooms on Earth. Changes in temperature and iron availability are expected to alter the intensity of SO phytoplankton blooms, but little is known about how environmental change will influence community composition and downstream biogeochemical processes. We performed experimental manipulations on surface ocean microbial communities from McMurdo Sound in the Ross Sea, with and without iron addition, at −0.5 °C, 3 °C, and 6 °C. We then examined nutrient uptake patterns as well as the growth and molecular responses of two dominant diatoms, Fragilariopsis and Pseudo-nitzschia, to these conditions. We found that nitrate uptake and primary productivity were elevated at increased temperature in the absence of iron addition, and were even greater at high temperature with added iron. Pseudo-nitzschia became more abundant under increased temperature without added iron, while Fragilariopsis required additional iron to benefit from warming. We attribute the apparent advantage Pseudo-nitzschia shows under warming to upregulation of iron-conserving photosynthetic processes, utilization of iron-economic nitrogen assimilation mechanisms, and increased iron uptake and storage. These data identify important molecular and physiological differences between dominant diatom groups and add to the growing body of evidence for Pseudo-nitzschia’s increasingly important role in warming SO ecosystems. This study also suggests that temperature-driven shifts in SO phytoplankton assemblages may increase utilization of the vast pool of excess nutrients in iron-limited SO surface waters, and thereby influence global nutrient distributions and carbon cycle.Significance Statement Phytoplankton assemblages contribute to the Southern Ocean’s ability to absorb atmospheric CO2, form the base of marine food webs, and shape the global distribution of macronutrients. Anthropogenic climate change is altering the SO environment, yet we do not fully understand how resident phytoplankton will react to this change. By comparing the responses of two prominent SO diatom groups to changes in temperature and iron in a natural community, we find that one group, Pseudo-nitzschia, grows better under warmer low-iron conditions by managing cellular iron demand and efficiently increasing photosynthetic capacity. This ability to grow and draw down nutrients in the face of warming, regardless of iron availability, may have major implications for ocean ecosystems and global nutrient and carbon cycles.Competing Interest StatementThe authors have declared no competing interest.View Full Text

ecology↗

bioRxiv2020

Dual thermal ecotypes detected within a nearly genetically-identical population of the unicellular marine cyanobacterium Synechococcus

The extent and ecological significance of intraspecific diversity within marine microbial populations is still poorly understood, and it remains unclear if such strain-level microdiversity will affect fitness and persistence in a rapidly changing ocean environment. In this study, we cultured 11 sympatric strains of the ubiquitous marine picocyanobacterium Synechococcus isolated from a Narragansett Bay (Rhode Island, USA) phytoplankton community thermal selection experiment. Despite all 11 isolates being highly similar (with average nucleotide identities of >99.9%, with 98.6-100% of the genome aligning), thermal performance curves revealed selection at warm and cool temperatures had subdivided the initial population into thermotypes with pronounced differences in maximum growth temperatures. Within the fine-scale genetic diversity that did exist within this population, the two divergent thermal ecotypes differed at a locus containing genes for the phycobilisome antenna complex. Our study demonstrates that present-day marine microbial populations can contain microdiversity in the form of cryptic but environmentally-relevant thermotypes that may increase their resilience to future rising temperatures. SignificanceNumerous studies exist comparing the responses of distinct taxonomic groups of marine microbes to a warming ocean (interspecific thermal diversity). For example, Synechococcus, a nearly globally distributed unicellular marine picocyanobacterium that makes significant contributions to oceanic primary productivity, contains numerous taxonomically distinct lineages with well documented temperature relationships. Little is known though about the diversity of functional responses to temperature within a given population where genetic similarity is high (intraspecific thermal diversity). This study suggests that understanding the extent of this functional intraspecific microdiversity is an essential prerequisite to predicting the resilience of biogeochemically essential microbial groups such as marine Synechococcus to a changing climate.

microbiology↗