Disentangling top-down drivers of mortality underlying diel population dynamics of Prochlorococcus in the North Pacific Subtropical Gyre.

Photosynthesis fuels primary production at the base of marine food webs. Yet, in many surface ocean ecosystems, diel-driven primary production is tightly coupled to daily loss. This tight coupling raises the question: which top-down drivers predominate in maintaining persistently stable picocyanobacterial populations over longer time scales? Motivated by high-frequency surface water measurements taken in the North Pacific Subtropical Gyre (NPSG), we developed multitrophic models to investigate bottom-up and top-down mechanisms underlying the balanced control of Prochlorococcus populations.

Building a queer- and trans-inclusive microbiology conference.

Microbiology conferences can be powerful places to build collaborations and exchange ideas, but for queer and transgender (trans) scientists, they can also become sources of alienation and isolation. Many conference organizers would like to create welcoming and inclusive events but feel ill-equipped to make this vision a reality, and a historical lack of representation of queer and trans folks in microbiology means we rarely occupy these key leadership roles ourselves. Looking more broadly, queer and trans scientists are systematically marginalized across scientific fields, leading to disparities in career outcomes, professional networks, and opportunities, as well as the loss of unique scientific perspectives at all levels.

Microbial and Viral Genome and Proteome Nitrogen Demand Varies across Multiple Spatial Scales within a Marine Oxygen Minimum Zone.

Nutrient availability can significantly influence microbial genomic and proteomic streamlining, for example, by selecting for lower nitrogen to carbon ratios. Oligotrophic open ocean microbes have streamlined genomic nitrogen requirements relative to those of their counterparts in nutrient-rich coastal waters. However, steep gradients in nutrient availability occur at meter-level, and even micron-level, spatial scales.

Complex marine microbial communities partition metabolism of scarce resources over the diel cycle.

Complex assemblages of microbes in the surface ocean are responsible for approximately half of global carbon fixation. The persistence of high taxonomic diversity despite competition for a small suite of relatively homogeneously distributed nutrients, that is, 'the paradox of the plankton', represents a long-standing challenge for ecological theory. Here we find evidence consistent with temporal niche partitioning of nitrogen assimilation processes over a diel cycle in the North Pacific Subtropical Gyre.

A Primer for Microbiome Time-Series Analysis.

Time-series can provide critical insights into the structure and function of microbial communities. The analysis of temporal data warrants statistical considerations, distinct from comparative microbiome studies, to address ecological questions. This primer identifies unique challenges and approaches for analyzing microbiome time-series.

Reevaluating the Salty Divide: Phylogenetic Specificity of Transitions between Marine and Freshwater Systems.

Marine and freshwater microbial communities are phylogenetically distinct, and transitions between habitat types are thought to be infrequent. We compared the phylogenetic diversity of marine and freshwater microorganisms and identified specific lineages exhibiting notably high or low similarity between marine and freshwater ecosystems using a meta-analysis of 16S rRNA gene tag-sequencing data sets. As expected, marine and freshwater microbial communities differed in the relative abundance of major phyla and contained habitat-specific lineages.

diDO-IPTL: A Peptide-Labeling Strategy for Precision Quantitative Proteomics.

We present an analytical strategy, dimethylation-deuteration and oxygen-exchange IPTL (diDO-IPTL), for high-precision, broad-coverage quantitative proteomics. The diDO-IPTL approach combines two advances in isobaric peptide terminal labeling (IPTL) methodology: first, a one-pot chemical labeling strategy for attaching isotopic tags to both the N- and C-termini of tryptic peptides, and second, a search engine (based on the Morpheus algorithm) optimized for identification and quantification of twinned peaks from peptide fragment ions in MS spectra. The diDO-IPTL labeling chemistry uses only high-purity, relatively inexpensive isotopic reagents (O water and deuterated formaldehyde) and requires no postlabeling cleanup or isotopic impurity corrections.