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1. Diversity, taxonomic composition, and functional aspects of fungal communities in living, senesced, and fallen leaves at five sites across North America

   https://doi.org/10.7717/peerj.2768  

   U’Ren, Jana M. ; Arnold, A. Elizabeth ( December 2016 , PeerJ)

   Fungal endophytes inhabit symptomless, living tissues of all major plant lineages to form one of earth’s most prevalent groups of symbionts. Many reproduce from senesced and/or decomposing leaves and can produce extracellular leaf-degrading enzymes, blurring the line between symbiotrophy and saprotrophy. To better understand the endophyte–saprotroph continuum we compared fungal communities and functional traits of focal strains isolated from living leaves to those isolated from leaves after senescence and decomposition, with a focus on foliage of woody plants in five biogeographic provinces ranging from tundra to subtropical scrub forest.

   We cultured fungi from the interior of surface-sterilized leaves that were living at the time of sampling (i.e., endophytes), leaves that were dead and were retained in plant canopies (dead leaf fungi, DLF), and fallen leaves (leaf litter fungi, LLF) from 3–4 species of woody plants in each of five sites in North America. Our sampling encompassed 18 plant species representing two families of Pinophyta and five families of Angiospermae. Diversity and composition of fungal communities within and among leaf life stages, hosts, and sites were compared using ITS-partial LSU rDNA data. We evaluated substrate use and enzyme activity by a subset of fungi isolated only from living tissues vs. fungi isolatedmore »only from non-living leaves.

   Across the diverse biomes and plant taxa surveyed here, culturable fungi from living leaves were isolated less frequently and were less diverse than those isolated from non-living leaves. Fungal communities in living leaves also differed detectably in composition from communities in dead leaves and leaf litter within focal sites and host taxa, regardless of differential weighting of rare and abundant fungi. All focal isolates grew on cellulose, lignin, and pectin as sole carbon sources, but none displayed ligninolytic or pectinolytic activityin vitro. Cellulolytic activity differed among fungal classes. Within Dothideomycetes, activity differed significantly between fungi from living vs. non-living leaves, but such differences were not observed in Sordariomycetes.

   Although some fungi with endophytic life stages clearly persist for periods of time in leaves after senescence and incorporation into leaf litter, our sampling across diverse biomes and host lineages detected consistent differences between fungal assemblages in living vs. non-living leaves, reflecting incursion by fungi from the leaf exterior after leaf death and as leaves begin to decompose. However, fungi found only in living leaves do not differ consistently in cellulolytic activity from those fungi detected thus far only in dead leaves. Future analyses should consider Basidiomycota in addition to the Ascomycota fungi evaluated here, and should explore more dimensions of functional traits and persistence to further define the endophytism-to-saprotrophy continuum.

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2. Phytoplankton community composition and biomass in the oligotrophic Gulf of Mexico

   https://doi.org/10.1093/plankt/fbab006  

   E Selph, Karen ; Swalethorp, Rasmus ; R Stukel, Michael ; B Kelly, Thomas ; N Knapp, Angela ; Fleming, Kelsey ; Hernandez, Tabitha ; R Landry, Michael ( March 2021 , Journal of Plankton Research)

   Campbell, Lisa (Ed.)

   Abstract Biomass and composition of the phytoplankton community were investigated in the deep-water Gulf of Mexico (GoM) at the edges of Loop Current anticyclonic eddies during May 2017 and May 2018. Using flow cytometry, high-performance liquid chromatography pigments and microscopy, we found euphotic zone integrated chlorophyll a of ~10 mg m−2 and autotrophic carbon ranging from 463 to 1268 mg m−2, dominated by picoplankton (<2 μm cells). Phytoplankton assemblages were similar to the mean composition at the Bermuda Atlantic Time-series Study site, but differed from the Hawaii Ocean Times-series site. GoM phytoplankton biomass was ~2-fold higher at the deep chlorophyll maximum (DCM) relative to the mixed layer (ML). Prochlorococcus and prymnesiophytes were the dominant taxa throughout the euphotic zone; however, other eukaryotic taxa had significant biomass in the DCM. Shallower DCMs were correlated with more prymnesiophytes and prasinophytes (Type 3) and reduced Prochlorococcus. These trends in ML and DCM taxonomic composition likely reflect relative nutrient supply—with ML populations relying on remineralized ammonium as a nitrogen source, and the taxonomically diverse DCM populations using more nitrate. These spatially separated phytoplankton communities represent different pathways for primary production, with a dominance of picoplankton in the ML and more nano- and microplankton at the DCM.
3. Independent iron and light limitation in a low-light-adapted Prochlorococcus from the deep chlorophyll maximum

   https://doi.org/10.1038/s41396-020-00776-y  

   Hawco, Nicholas J. ; Fu, Feixue ; Yang, Nina ; Hutchins, David A. ; John, Seth G. ( September 2020 , The ISME Journal)

   Throughout the open ocean, a minimum in dissolved iron concentration (dFe) overlaps with the deep chlorophyll maximum (DCM), which marks the lower limit of the euphotic zone. Maximizing light capture in these dim waters is expected to require upregulation of Fe-bearing photosystems, further depleting dFe and possibly leading to co-limitation by both iron and light. However, this effect has not been quantified for important phytoplankton groups likeProchlorococcus, which contributes most of the productivity in the oligotrophic DCM. Here, we present culture experiments withProchlorococcusstrain MIT1214, a member of the Low Light 1 ecotype isolated from the DCM in the North Pacific subtropical gyre. Under a matrix of iron and irradiance matching those found at the DCM, the ratio of Fe to carbon inProchlorococcusMIT1214 cells ranged from 10–40 × 10⁻⁶ mol Fe:mol C and increased with light intensity and growth rate. These results challenge theoretical models predicting highest Fe:C at lowest light intensity, and are best explained by a large photosynthetic Fe demand that is not downregulated at higher light. To sustain primary production in the DCM with the rigid Fe requirements of low-light-adaptedProchlorococcus, dFe must be recycled rapidly and at high efficiency.
4. Siderophores as an iron source for picocyanobacteria in deep chlorophyll maximum layers of the oligotrophic ocean

   https://doi.org/10.1038/s41396-022-01215-w  

   Hogle, Shane L. ; Hackl, Thomas ; Bundy, Randelle M. ; Park, Jiwoon ; Satinsky, Brandon ; Hiltunen, Teppo ; Biller, Steven ; Berube, Paul M. ; Chisholm, Sallie W. ( March 2022 , The ISME Journal)

   ProchlorococcusandSynechococcusare the most abundant photosynthesizing organisms in the oceans. Gene content variation among picocyanobacterial populations in separate ocean basins often mirrors the selective pressures imposed by the region’s distinct biogeochemistry. By pairing genomic datasets with trace metal concentrations from across the global ocean, we show that the genomic capacity for siderophore-mediated iron uptake is widespread inSynechococcusand low-light adaptedProchlorococcuspopulations from deep chlorophyll maximum layers of iron-depleted regions of the oligotrophic Pacific and S. Atlantic oceans:Prochlorococcussiderophore consumers were absent in the N. Atlantic ocean (higher new iron flux) but constituted up to half of allProchlorococcusgenomes from metagenomes in the N. Pacific (lower new iron flux). Picocyanobacterial siderophore consumers, like many other bacteria with this trait, also lack siderophore biosynthesis genes indicating that they scavenge exogenous siderophores from seawater. Statistical modeling suggests that the capacity for siderophore uptake is endemic to remote ocean regions where atmospheric iron fluxes are the smallest, especially at deep chlorophyll maximum and primary nitrite maximum layers. We argue that abundant siderophore consumers at these two common oceanographic features could be a symptom of wider community iron stress, consistent with prior hypotheses. Our results provide a clear example of iron as a selective force driving the evolution ofmore »marine picocyanobacteria.

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5. Efficient and cost-effective bacterial mRNA sequencing from low input samples through ribosomal RNA depletion

   https://doi.org/10.1186/s12864-020-07134-4  

   Wangsanuwat, Chatarin ; Heom, Kellie A. ; Liu, Estella ; O’Malley, Michelle A. ; Dey, Siddharth S. ( October 2020 , BMC Genomics)

   RNA sequencing is a powerful approach to quantify the genome-wide distribution of mRNA molecules in a population to gain deeper understanding of cellular functions and phenotypes. However, unlike eukaryotic cells, mRNA sequencing of bacterial samples is more challenging due to the absence of a poly-A tail that typically enables efficient capture and enrichment of mRNA from the abundant rRNA molecules in a cell. Moreover, bacterial cells frequently contain 100-fold lower quantities of RNA compared to mammalian cells, which further complicates mRNA sequencing from non-cultivable and non-model bacterial species. To overcome these limitations, we report EMBR-seq (Enrichment of mRNA by Blocked rRNA), a method that efficiently depletes 5S, 16S and 23S rRNA using blocking primers to prevent their amplification.

   EMBR-seq results in 90% of the sequenced RNA molecules from anE. coliculture deriving from mRNA. We demonstrate that this increased efficiency provides a deeper view of the transcriptome without introducing technical amplification-induced biases. Moreover, compared to recent methods that employ a large array of oligonucleotides to deplete rRNA, EMBR-seq uses a single or a few oligonucleotides per rRNA, thereby making this new technology significantly more cost-effective, especially when applied to varied bacterial species. Finally, compared to existing commercial kits for bacterialmore »rRNA depletion, we show that EMBR-seq can be used to successfully quantify the transcriptome from more than 500-fold lower starting total RNA.

   EMBR-seq provides an efficient and cost-effective approach to quantify global gene expression profiles from low input bacterial samples.

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