Biology subjects

Chisholm, S. W.

Publications and source records attributed to Chisholm, S. W..

29 records · Page 2Linked to original sources

bioRxiv2020

Novel integrative elements and genomic plasticity in ocean ecosystems

Horizontal gene transfer accelerates microbial evolution, promoting diversification and adaptation. The globally abundant marine cyanobacterium Prochlorococcus has a highly streamlined genome with frequent gene exchange reflected in its extensive pangenome. The source of its genomic variability, however, remains elusive since most cells lack the common mechanisms that enable horizontal gene transfer, including conjugation, transformation, plasmids and prophages. Examining 623 genomes, we reveal a diverse system of mobile genetic elements - cargo-carrying transposons we named tycheposons - that shape Prochlorococcus genomic plasticity. The excision and integration of tycheposons at seven tRNA genes drive the remodeling of larger genomic islands containing most of Prochlorococcus flexible genes. Most tycheposons carry genes important for niche differentiation through nutrient acquisition; others appear similar to phage parasites. Tycheposons are highly enriched in extracellular vesicles and phage particles in ocean samples, suggesting efficient routes for their dispersal, transmission and propagation. Supported by evidence for similar elements in other marine microbes, our work underpins the role of vesicle- and virus-mediated transfer of mobile genetic elements in the diversification and adaptation of microbes in dilute aquatic environments - adding a significant piece to the puzzle of what governs microbial evolution in the planets largest habitat.

microbiology↗

bioRxiv2020

Prochlorococcus extracellular vesicles: Molecular composition and adsorption to diverse microbes

Extracellular vesicles are small (~50-200 nm diameter) membrane-bound structures released by cells from all domains of life. While vesicles are abundant in the oceans, our understanding of their functions, both for cells themselves and the emergent ecosystem, is in its infancy. To advance this understanding, we analyzed the lipid, protein, and metabolite content of vesicles produced by the marine cyanobacterium Prochlorococcus. We show that Prochlorococcus exports an enormous array of cellular compounds into the surrounding seawater within vesicles. Vesicles produced by two different strains contain some materials in common, but also display numerous strain-specific differences, reflecting functional complexity within natural vesicle populations. Prochlorococcus vesicles contain active enzymes, indicating that they can mediate extracellular biogeochemical reactions in the ocean. We demonstrate that vesicles from Prochlorococcus and other bacteria associate with diverse microbes including the most abundant marine bacterium, Pelagibacter. Our observations suggest that vesicles may play diverse functional roles in the oceans, including but not limited to mediating energy and nutrient transfers, catalyzing extracellular biochemical reactions, and mitigating toxicity of reactive oxygen species. These findings indicate that a portion of dissolved compounds in the oceans are not truly dissolved, but are instead packaged within locally structured, particulate vesicles.

microbiology↗

bioRxiv2020

Phosphonate production by marine microbes: exploring new sources and potential function

Phosphonates, organic compounds with a C-P bond, constitute 20-25% of phosphorus in high molecular weight dissolved organic matter and are a significant phosphorus source for marine microbes. However, little is known about phosphonate sources, biological function, or biogeochemical cycling. Here, we determine the biogeographic distribution and prevalence of phosphonate biosynthesis potential using thousands of genomes and metagenomes from the upper 250 meters of the global ocean. Potential phosphonate producers are taxonomically diverse, occur in widely distributed and abundant marine lineages (including SAR11 and Prochlorococcus) and their abundance increases with depth. Within those lineages, phosphonate biosynthesis and catabolism pathways are mutually exclusive, indicating functional niche partitioning of organic phosphorus cycling in the marine microbiome. Surprisingly, one strain of Prochlorococcus (SB) can allocate more than 40% of its cellular P-quota towards phosphonate production. Chemical analyses and genomic evidence suggest that phosphonates in this strain are incorporated into surface layer glycoproteins that may act to reduce mortality from grazing or viral infection. Although phosphonate production is a low-frequency trait in Prochlorococcus populations (~ 5% of genomes), experimentally derived production rates suggest that Prochlorococcus could produce a significant fraction of the total phosphonate in the oligotrophic surface ocean. These results underscore the global biogeochemical impact of even relatively rare functional traits in abundant groups like Prochlorococcus and SAR11.

biochemistry↗

bioRxiv2020

Coping with darkness: The adaptive response of marine picocyanobacteria to repeated light energy deprivation

The picocyanobacteria Prochlorococcus and Synechococcus are found throughout the oceans euphotic zone, where the daily light:dark cycle drives their physiology. Periodic deep mixing events can, however, move cells below this zone, depriving them of light for extended periods of time. Here we demonstrate that Prochlorococcus and Synechococcus can adapt to tolerate repeated periods of light energy deprivation. Cyanobacterial cultures kept in the dark for 3 days and then returned to the light initially required 18-26 days to resume growth, but after multiple rounds of dark exposure the strains began to regrow after only 1-2 days. This dark-tolerant phenotype was stable and heritable; cultures retained the trait across at least 18-21 generations even when grown in a standard 13:11 light:dark cycle. We found no genetic differences between the dark-tolerant and parental strains of Prochlorococcus NATL2A, indicating that an epigenetic change is responsible for the adaptation. To begin to explore this possibility, we asked whether DNA methylation - an epigenetic mechanism in bacteria - occurs in Prochlorococcus. LC-MS/MS analysis showed that while DNA methylations, including 6mA and 5mC, are found in some other Prochlorococcus strains, no methylations were detected in either the parental or dark-tolerant strain used in our experiments -i.e. the NATL2A strain. These findings suggest that Prochlorococcus utilizes a yet-to-be-determined epigenetic mechanism to adapt to the stress of extended light energy deprivation.

microbiology↗

bioRxiv2020

Microbial Diversity of Co-occurring Heterotrophs in Cultures of Marine Picocyanobacteria

Prochlorococcus and Synechococcus are responsible for around 10% of global net primary productivity, serving as part of the foundation of marine food webs. Heterotrophic bacteria are often co-isolated with these picocyanobacteria in seawater enrichment cultures that contain no added organic carbon; heterotrophs grow on organic carbon supplied by the photolithoautotrophs. We have maintained these cultures of Prochlorococcus and Synechococcus for 100s to 1000s of generations; they represent ideal microcosms for examining the selective pressures shaping autotroph/heterotroph interactions. Here we examine the diversity of heterotrophs in 74 enrichment cultures of these picocyanobacteria obtained from diverse areas of the global oceans. Heterotroph community composition differed between clades and ecotypes of the autotrophic hosts but there was significant overlap in heterotroph community composition. Differences were associated with timing, location, depth, and methods of isolation, suggesting the particular conditions surrounding isolation have a persistent effect on long-term culture composition. The majority of heterotrophs in the cultures are rare in the global ocean; enrichment conditions favor the opportunistic outgrowth of these rare bacteria. We did find a few examples, such as heterotrophs in the family Rhodobacteraceae, that are ubiquitous and abundant in cultures and in the global oceans; their abundance in the wild is also positively correlated with that of picocyanobacteria. Collectively, the cultures converged on similar compositions, likely from bottlenecking and selection that happens during the early stages of enrichment for the picocyanobacteria. We highlight the potential for examining ecologically relevant relationships by identifying patterns of distribution of culture-enriched organisms in the global oceans. IMPORTANCEOne of the biggest challenges in marine microbial ecology is to begin to understand the rules that govern the self-assembly of these complex communities. The picocyanobacteria Prochlorococcus and Synechococcus comprise the most numerous photosynthetic organisms in the sea and supply a significant fraction of the organic carbon that feeds diverse heterotrophic microbes. When initially isolated into cultures, Prochlorococcus and Synechococcus carry with them select heterotrophic microorganisms that depend on them for organic carbon. The cultures self-assemble into stable communities of diverse microorganisms and are microcosms for understanding microbial interdependencies. Primarily faster-growing, relatively rare, copiotrophic heterotrophic bacteria - as opposed to oligotrophic bacteria that are abundant in picocyanobacterial habitats - are selected for in these cultures, suggesting that these copiotrophs experience these cultures as they would high carbon fluxes associated with particles, phycospheres of larger cells, or actual attachment to picocyanobacteria in the wild.

microbiology↗

bioRxiv2020

Association of lanthipeptide genes with TnpAREP transposases in marine picocyanobacteria

Lanthipeptides are a family of ribosomally synthesized, post-translationally modified peptides that are widespread among bacteria, typically functioning as antibacterials. The marine picocyanobacteria Prochlorococcus and Synechococcus produce an unusual and diverse set of lanthipeptides of unknown function called prochlorosins. While well-studied model bacteria produce one or two different molecules of this type, a single picocyanobacterium can produce as many as 80; the community of picocyanobacteria in a single milliliter of seawater can collectively encode up to 10,000 prochlorosins. The molecular events that led to this expansion and diversification of the lanthipeptide repertoire in picocyanobacteria - the numerically dominant photosynthesizers in the oceans - is unknown. We present evidence for an unusual association between prochlorosin genes with a single-stranded DNA transposase belonging to the TnpAREP family. The genes co-occur and co-localize across the phylogeny of marine picocyanobacteria forming a distinct association pattern within genomes, most likely resulting from the transposase activity. Given the role of TnpAREP homologs in other bacteria, we propose - based on genomic structures - that they contribute to the creation of the prochlorosin structural diversity through a diversifying recombination mechanism. Post-submission noteSince the original submission of this manuscript to bioRxiv, we have refined our phylogenetic analysis of the TnpA-REP transposases and we do not find strong evidence for or against a causal relationship between the presence of TnpA-REP transposases and the expansion and diversification of lanthipeptides genes. While the genetic association described in the manuscript remains valid, adjacent TnpA-REP and Prochlorosins do not appear phylogenetically linked, which might simply be the consequence of high rates of recombination for both genes. More genomic data are needed to untangle the driving force behind the lanthipeptide gene expansion in marine picocyanobacteria. IMPORTANCEOnly a few mechanisms have been described that promote the diversification of a targeted gene region in bacteria. We present indirect evidence that the TnpAREP transposases associated with prochlorosins in picocyanobacteria could represent a novel such mechanism, and explain the extreme expansion and diversification of prochlorosins in this abundant marine microbe.

microbiology↗

bioRxiv2020

Frequency of mispackaging of Prochlorococcus DNA by cyanophage

Prochlorococcus cells are the numerically dominant phototrophs in the open ocean. Cyanophages that infect them are thus a notable fraction of the total viral population in the euphotic zone, and, as vehicles of horizontal gene transfer, appear to drive their evolution. Here we examine the propensity of three cyanophages - a podovirus, a siphovirus, and a myovirus - to mispackage host DNA in their capsids while infecting Prochlorococcus, the first step in phage-mediated horizontal gene transfer. We find the mispackaging frequencies are distinctly different among the three phages. Myoviruses mispackage host DNA at low and stable frequencies, while podo- and siphoviruses vary in their mispackaging frequencies by orders of magnitude depending on growth light intensity. We attribute this difference to the concentration of intracellular reactive oxygen species and protein synthesis rates. Based on our findings, we propose a model of mispackaging frequency determined by the imbalance between the production of capsids and the number of phage genome copies during infection.

microbiology↗

bioRxiv2019

Toward a genetic system in the marine cyanobacterium Prochlorococcus

As the smallest and most abundant primary producer in the oceans, the cyanobacterium Prochlorococcus is of interest to diverse branches of science. For the past 30 years, research on this minimal phototroph has led to a growing understanding of biological organization across multiple scales, from the genome to the global ocean ecosystem. Progress in understanding drivers of its diversity and ecology, as well as molecular mechanisms underpinning its streamlined simplicity, has been hampered by the inability to manipulate these cells genetically.\n\nMultiple attempts have been made to develop an efficient genetic transformation method for Prochlorococcus over the years; all have been unsuccessful to date, despite some success with their close relative, Synechococcus. To avoid the pursuit of unproductive paths, we report here what has not worked in our hands, as well as our progress developing a method to screen the most efficient electroporation parameters for optimal DNA delivery into Prochlorococcus cells. We also report a novel protocol for obtaining axenic colonies and a new method for differentiating live and dead cells. The electroporation method can be used to optimize DNA delivery into any bacterium, making it a useful tool for advancing transformation systems in other genetically recalcitrant microorganisms.

microbiology↗

bioRxiv2018

Co-culture and biogeography of Prochlorococcus and SAR11

Prochlorococcus and SAR11 are among the smallest and most abundant organisms on Earth. With a combined global population of about 2.7 x 1028 cells, they numerically dominate bacterioplankton communities in oligotrophic ocean gyres and yet they have never been grown together in vitro. Here we describe co-cultures of Prochlorococcus and SAR11 isolates representing both high- and low-light adapted clades. We examined: (1) the influence of Prochlorococcus on the growth of SAR11 and vice-versa, (2) whether Prochlorococcus can meet specific nutrient requirements of SAR11, and (3) how co-culture dynamics vary when Prochlorococcus is grown with SAR11 compared with sympatric copiotrophic bacteria. SAR11 grew as much as 70% faster in the presence of Prochlorococcus, while the growth of the latter was unaffected. When Prochlorococcus populations entered stationary phase, SAR11 abundances decreased dramatically. In parallel experiments with copiotrophic bacteria however, the heterotrophic partner increased in abundance as Prochlorococcus densities leveled off. The presence of Prochlorococcus was able to meet SAR11s central requirement for organic carbon, but not reduced sulfur. Prochlorococcus strain MIT9313, but not MED4, could meet the unique glycine requirement of SAR11, likely due to production and release of glycine betaine by MIT9313. Evidence suggests that Prochlorococcus MIT9313 may also compete with SAR11 for the uptake of 3-dimethylsulfoniopropionate (DMSP). To place our results in context, we assessed the relative contribution of Prochlorococcus and SAR11 genome equivalents to those of identifiable bacteria and archaea in over 800 marine metagenomes. At many locations, more than half of the identifiable genome equivalents in the euphotic zone belonged to Prochlorococcus and SAR11 - highlighting the biogeochemical potential of these two groups.

microbiology↗

bioRxiv2018

Emergence of trait variability through the lens of nitrogen assimilation in Prochlorococcus

Intraspecific trait variability has important consequences for the function and stability of marine ecosystems. The marine cyanobacterium Prochlorococcus is a useful model system for understanding how trait variability emerges within microbial species: Its functional diversity is overlaid on measurable environmental gradients, providing a powerful lens into large-scale evolutionary processes. Here we examine variation in the ability to use nitrate across hundreds of Prochlorococcus genomes to better understand the modes of evolution influencing the allocation of ecologically important functions within microbial species. We find that nitrate assimilation genes are absent in basal lineages of Prochlorococcus but occur at an intermediate frequency that is randomly distributed within recently emerged clades. The distribution of nitrate assimilation genes within clades appears largely governed by vertical inheritance, stochastic gene loss, and homologous recombination among closely related cells. By mapping this process onto a model of Prochlorococcus macroevolution, we propose that niche-constructing adaptive radiations and subsequent niche partitioning set the stage for loss of nitrate assimilation genes from basal lineages as they specialized to lower light levels. Retention of these genes in recently emerged lineages has likely been facilitated by selection as they sequentially partitioned into niches where nitrate assimilation conferred a fitness benefit.

evolutionary biology↗

bioRxiv2016

Nitrogen cost minimization is promoted by structural changes in the transcriptome of N deprived Prochlorococcus cells

Prochlorococcus is a globally abundant marine cyanobacterium with many adaptations that reduce cellular nutrient requirements, facilitating growth in its nutrient-poor environment. One such genomic adaptation is the preferential utilization of amino acids containing fewer N-atoms, which minimizes cellular nitrogen requirements. We predicted that transcriptional regulation might be used to further reduce cellular N budgets during transient N limitation. To explore this, we compared transcription start sites (TSSs) in Prochlorococcus MED4 under N-deprived and N-replete conditions. Of 64 genes with primary and internal TSSs in both conditions, N-deprived cells initiated transcription downstream of primary TSSs more frequently than N-replete cells. Additionally, 117 genes with only an internal TSS demonstrated increased internal transcription under N-deprivation. These shortened transcripts encode predicted proteins with ~5-20% less N content compared to full-length transcripts. We hypothesized that low translation rates, which afford greater control over protein abundances, would be beneficial to relatively slow-growing organisms like Prochlorococcus. Consistent with this idea, we found that Prochlorococcus exhibits greater usage of glycine-glycine motifs, which cause translational pausing, when compared to faster growing microbes. Our findings indicate that structural changes occur within the Prochlorococcus MED4 transcriptome during N-deprivation, potentially altering the size and structure of proteins expressed under nutrient limitation.

genomics↗