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1. Pontiella agarivorans sp. nov., a novel marine anaerobic bacterium capable of degrading macroalgal polysaccharides and fixing nitrogen

   https://doi.org/10.1128/aem.00914-23  

   Liu, Na ; Kivenson, Veronika ; Peng, Xuefeng ; Cui, Zhisong ; Lankiewicz, Thomas S ; Gosselin, Kelsey M ; English, Chance J ; Blair, Elaina M ; O'Malley, Michelle A ; Valentine, David L ( February 2024 , Applied and Environmental Microbiology)

   Glass, Jennifer B (Ed.)

   Marine macroalgae produce abundant and diverse polysaccharides, which contribute substantially to the organic matter exported to the deep ocean. Microbial degradation of these polysaccharides plays an important role in the turnover of macroalgal biomass. Various members of thePlanctomycetes-Verrucomicrobia-Chlamydia(PVC) superphylum are degraders of polysaccharides in widespread anoxic environments. In this study, we isolated a novel anaerobic bacterial strain NLcol2^Tfrom microbial mats on the surface of marine sediments offshore Santa Barbara, CA, USA. Based on 16S ribosomal RNA (rRNA) gene and phylogenomic analyses, strain NLcol2^Trepresents a novel species within thePontiellagenus in theKiritimatiellotaphylum (within the PVC superphylum). Strain NLcol2^Tis able to utilize various monosaccharides, disaccharides, and macroalgal polysaccharides such as agar and ɩ-carrageenan. A near-complete genome also revealed an extensive metabolic capacity for anaerobic degradation of sulfated polysaccharides, as evidenced by 202 carbohydrate-active enzymes (CAZymes) and 165 sulfatases. Additionally, its ability of nitrogen fixation was confirmed by nitrogenase activity detected during growth on nitrogen-free medium, and the presence of nitrogenases (nifDKH) encoded in the genome. Based on the physiological and genomic analyses, this strain represents a new species of bacteria that may play an important role in the degradation of macroalgal polysaccharides and with relevance to the biogeochemical cycling of carbon, sulfur, and nitrogen in marine environments. Strain NLcol2^T(= DSM 113125^T= MCCC 1K08672^T) is proposed to be the type strain of a novel species in thePontiellagenus, and the namePontiella agarivoranssp. nov. is proposed.

   Growth and intentional burial of marine macroalgae is being considered as a carbon dioxide reduction strategy but elicits concerns as to the fate and impacts of this macroalgal carbon in the ocean. Diverse heterotrophic microbial communities in the ocean specialize in these complex polymers such as carrageenan and fucoidan, for example, members of theKiritimatiellotaphylum. However, only four type strains within the phylum have been cultivated and characterized to date, and there is limited knowledge about the metabolic capabilities and functional roles of related organisms in the environment. The new isolate strain NLcol2^Texpands the known substrate range of this phylum and further reveals the ability to fix nitrogen during anaerobic growth on macroalgal polysaccharides, thereby informing the issue of macroalgal carbon disposal.

    

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2. Assessing the utility of SoilGrids250 for biogeographic inference of plant populations

   https://doi.org/10.1002/ece3.10986  

   Miller, Tony ; Blackwood, Christopher B. ; Case, Andrea L. ( March 2024 , Ecology and Evolution)

   Inclusion of edaphic conditions in biogeographical studies typically provides a better fit and deeper understanding of plant distributions. Increased reliance on soil data calls for easily accessible data layers providing continuous soil predictions worldwide. Although SoilGrids provides a potentially useful source of predicted soil data for biogeographic applications, its accuracy for estimating the soil characteristics experienced by individuals in small‐scale populations is unclear. We used a biogeographic sampling approach to obtain soil samples from 212 sites across the midwestern and eastern United States, sampling only at sites where there was a population of one of the 22 species inLobeliasect.Lobelia. We analyzed six physical and chemical characteristics in our samples and compared them with predicted values from SoilGrids. Across all sites and species, soil texture variables (clay, silt, sand) were better predicted by SoilGrids (R²: .25–.46) than were soil chemistry variables (carbon and nitrogen,R² ≤ .01; pH,R²: .19). While SoilGrids predictions rarely matched actual field values for any variable, we were able to recover qualitative patterns relating species means and population‐level plant characteristics to soil texture and pH. Rank order of species mean values from SoilGrids and direct measures were much more consistent for soil texture (Spearmanr_S = .74–.84; allp < .0001) and pH (r_S = .61,p = .002) than for carbon and nitrogen (p > .35). Within the speciesL. siphilitica, a significant association, known from field measurements, between soil texture and population sex ratios could be detected using SoilGrids data, but only with large numbers of sites. Our results suggest that modeled soil texture values can be used with caution in biogeographic applications, such as species distribution modeling, but that soil carbon and nitrogen contents are currently unreliable, at least in the region studied here.

    

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3. Phylogenomics of the genus Populus reveals extensive interspecific gene flow and balancing selection

   https://doi.org/10.1111/nph.16215  

   Wang, Mingcheng ; Zhang, Lei ; Zhang, Zhiyang ; Li, Mengmeng ; Wang, Deyan ; Zhang, Xu ; Xi, Zhenxiang ; Keefover‐Ring, Ken ; Smart, Lawrence_B ; DiFazio, Stephen_P ; et al ( October 2019 , New Phytologist)

   Phylogenetic analysis is complicated by interspecific gene flow and the presence of shared ancestral polymorphisms, particularly those maintained by balancing selection. In this study, we aimed to examine the prevalence of these factors during the diversification ofPopulus, a model tree genus in the Northern Hemisphere.

   We constructed phylogenetic trees of 29Populustaxa using 80 individuals based on re‐sequenced genomes. Our species tree analyses recovered four main clades in the genus based on consensus nuclear phylogenies, but in conflict with the plastome phylogeny. A few interspecific relationships remained unresolved within the multiple‐species clade because of inconsistent gene trees. Our results indicated that gene flow has been widespread within each clade and also occurred among the four clades during their early divergence.

   We identified 45 candidate genes with ancient polymorphisms maintained by balancing selection. These genes were mainly associated with mating compatibility, growth and stress resistance.

   Both gene flow and selection‐mediated ancient polymorphisms are prevalent in the genusPopulus. These are potentially important contributors to adaptive variation. Our results provide a framework for the diversification of model tree genus that will facilitate future comparative studies.

    

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4. Diverse nitrogen cycling pathways across a marine oxygen gradient indicate nitrogen loss coupled to chemoautotrophic activity

   https://doi.org/10.1111/1462-2920.15187  

   Suter, Elizabeth A. ; Pachiadaki, Maria G. ; Montes, Enrique ; Edgcomb, Virginia P. ; Scranton, Mary I. ; Taylor, Craig D. ; Taylor, Gordon T. ( August 2020 , Environmental Microbiology)

   Genetic markers and geochemical assays of microbial nitrogen cycling processes, including autotrophic and heterotrophic denitrification, anammox, ammonia oxidation, and nitrite oxidation, were examined across the oxycline, suboxic, and anoxic zones of the Cariaco Basin, Venezuela. Ammonia and nitrite oxidation genes were expressed through the entire gradient. Transcripts associated with autotrophic and heterotrophic denitrifiers were mostly confined to the suboxic zone and below but were also present in particles in the oxycline. Anammox genes and transcripts were detected over a narrow depth range near the bottom of the suboxic zone and coincided with secondary NO₂⁻maxima and available NH₄⁺. Dissolved inorganic nitrogen (DIN) amendment incubations and comparisons between our sampling campaigns suggested that denitrifier activity may be closely coupled with NO₃⁻availability. Expression of denitrification genes at depths of high rates of chemoautotrophic carbon fixation and phylogenetic analyses of nitrogen cycling genes and transcripts indicated a diverse array of denitrifiers, including chemoautotrophs capable of using NO₃⁻to oxidize reduced sulfur species. Thus, results suggest that the Cariaco Basin nitrogen cycle is influenced by autotrophic carbon cycling in addition to organic matter oxidation and anammox.

    

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5. Identification and Expression Analyses of the Nitrate Transporter Gene ( NRT2 ) Family Among Skeletonema species (Bacillariophyceae)

   https://doi.org/10.1111/jpy.12896  

   Kang, Lee‐Kuo ; Rynearson, Tatiana A. ; Kroth, ed., P. ( August 2019 , Journal of Phycology)

   High‐affinity nitrate transporters are considered to be the major transporter system for nitrate uptake in diatoms. In the diatom genusSkeletonema, three forms of genes encoding high‐affinity nitrate transporters (NRT2) were newly identified from transcriptomes generated as part of the marine microbial eukaryote transcriptome sequencing project. To examine the expression of each form ofNRT2under different nitrogen environments, laboratory experiments were conducted under nitrate‐sufficient, ammonium‐sufficient, and nitrate‐limited conditions using three ecologically importantSkeletonemaspecies:S. dohrnii,S. menzelii,andS. marinoi. Primers were developed for eachNRT2form and species and Q‐RT‐PCRwas performed. For eachNRT2form, the threeSkeletonemaspecies had similar transcriptional patterns. The transcript levels ofNRT2:1were significantly elevated under nitrogen‐limited conditions, but strongly repressed in the presence of ammonium. The transcript levels ofNRT2:2were also repressed by ammonium, but increased 5‐ to 10‐fold under nitrate‐sufficient and nitrogen‐limited conditions. Finally, the transcript levels ofNRT2:3did not vary significantly under various nitrogen conditions, and behaved more like a constitutively expressed gene. Based on the observed transcript variation amongNRT2forms, we propose a revised model describing nitrate uptake kinetics regulated by multiple forms of nitrate transporter genes in response to various nitrogen conditions inSkeletonema. The differentialNRT2transcriptional responses among species suggest that species‐specific adaptive strategies exist within this genus to cope with environmental changes.

    

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