More Like this

1. Ecology eclipses phylogeny as a major driver of nematode parasite community structure in a graminivorous primate

   https://doi.org/10.1111/1365-2435.13603  

   Schneider‐Crease, India ; Beehner, Jacinta C. ; Bergman, Thore J. ; Gomery, Megan A. ; Koklic, Lia ; Lu, Amy ; Snyder‐Mackler, Noah ; Barribeau, ed., Seth ( June 2020 , Functional Ecology)

   Understanding how ecology and phylogeny shape parasite communities can inform parasite control and wildlife conservation initiatives while contributing to the study of host species evolution.

   We tested the relative strengths of phylogeny and ecology in driving parasite community structure in a host whose ecology diverges significantly from that of its closest phylogenetic relatives.

   We characterized the gastrointestinal (GI) parasite community of wild geladasTheropithecus gelada, primates that are closely related to baboons but specialized to graminovory in the Ethiopian Highlands.

   Geladas exhibited very constrained GI parasite communities: only two genera (OesophagostomumandTrichostrongylus) were identified across 305 samples. This is far below the diversity reported for baboons (Papiospp.) and at the low end of the range of domestic grazers (e.g.Bos taurus,Ovis aries) inhabiting the same region and ecological niche.

   Using deep amplicon sequencing, we identified 15 amplicon sequence variants (ASVs) within the two genera, seven of which matched toOesophagostomumsp., seven toTrichostrongylussp., and one toT. vitrinus.

   Population was an important predictor of ASV richness. Geladas in the most ecologically disturbed area of the national park exhibited approximately four times higher ASV richness than geladas at a less disturbed location within the park.

   In this system, ecology was a stronger predictor of parasite community structure than was phylogeny, with geladas sharing more elements of their parasite communities with other grazers in the same area than with closely related sister taxa.

   A freePlain Language Summarycan be found within the Supporting Information of this article.

    

   more » « less
2. Soil microbial legacy drives crop diversity advantage: Linking ecological plant–soil feedback with agricultural intercropping

   https://doi.org/10.1111/1365-2664.13802  

   Wang, Guangzhou ; Bei, Shuikuan ; Li, Jianpeng ; Bao, Xingguo ; Zhang, Jiudong ; Schultz, Peggy A. ; Li, Haigang ; Li, Long ; Zhang, Fusuo ; Bever, James D. ; et al ( December 2020 , Journal of Applied Ecology)

   Although the importance of the soil microbiome in mediating plant community structures and functions has been increasingly emphasized in ecological studies, the biological processes driving crop diversity overyielding remain unexplained in agriculture. Based on the plant–soil feedback (PSF) theory and method, we quantified to what extent and how soil microbes contributed to intercropping overyielding.

   Soils were collected as inocula and sequenced from a unique 10‐year field experiment, consisting of monoculture, intercropping and rotation planted with wheat (Triticum aestivum), maize (Zea mays)or faba bean (Vicia faba). A PSF greenhouse study was conducted to test microbial effects on three crops' growth in monoculture or intercropping.

   In wheat & faba bean (W&F) and maize & faba bean (M&F) systems, soil microbes drove intercropping overyielding compared to monoculture, with 28%–51% of the overyielding contributed by microbial legacies. The overyielding effects resulted from negative PSFs in both systems, as crops, in particular faba bean grew better in soils conditioned by other crops than itself. Moreover, faba bean grew better in soils from intercropping or rotation than from the average of monocultures, indicating a strong positive legacy effect of multispecies cropping systems. However, with positive PSF and negative legacy benefit effect of intercropping/rotation, we did not observe significant overyielding in the W&M system.

   With more bacterial and fungal dissimilarities by metabarcoding in heterospecific than its own soil, the better it improved faba bean growth. More detailed analysis showed faba bean monoculture soil accumulated more putative pathogens with higherFusariumrelative abundance and moreFusarium oxysporumgene copies by qPCR, while in heterospecific soils, there were less pathogenic effects when cereals were engaged. Further analysis in maize/faba bean intercropping also showed an increase of rhizobia relative abundance.

   Synthesis and applications. Our results demonstrate a soil microbiome‐mediated advantage in intercropping through suppression of the negative PSF of pathogens and increasing beneficial microbes. As microbial mediation of overyielding is context‐dependent, we conclude that the dynamics of both beneficial and pathogenic microbes should be considered in designing cropping systems for sustainable agriculture, particularly including combinations of legumes and cereals.

    

   more » « less
3. Toward a global reference database of COI barcodes for marine zooplankton

   https://doi.org/10.1007/s00227-021-03887-y  

   Bucklin, Ann ; Peijnenburg, Katja T. C. A. ; Kosobokova, Ksenia N. ; O’Brien, Todd D. ; Blanco-Bercial, Leocadio ; Cornils, Astrid ; Falkenhaug, Tone ; Hopcroft, Russell R. ; Hosia, Aino ; Laakmann, Silke ; et al ( May 2021 , Marine Biology)

   Characterization of species diversity of zooplankton is key to understanding, assessing, and predicting the function and future of pelagic ecosystems throughout the global ocean. The marine zooplankton assemblage, including only metazoans, is highly diverse and taxonomically complex, with an estimated ~28,000 species of 41 major taxonomic groups. This review provides a comprehensive summary of DNA sequences for the barcode region of mitochondrial cytochrome oxidase I (COI) for identified specimens. The foundation of this summary is the MetaZooGene Barcode Atlas and Database (MZGdb), a new open-access data and metadata portal that is linked to NCBI GenBank and BOLD data repositories. The MZGdb provides enhanced quality control and tools for assembling COI reference sequence databases that are specific to selected taxonomic groups and/or ocean regions, with associated metadata (e.g., collection georeferencing, verification of species identification, molecular protocols), and tools for statistical analysis, mapping, and visualization. To date, over 150,000 COI sequences for ~ 5600 described species of marine metazoan plankton (including holo- and meroplankton) are available via the MZGdb portal. This review uses the MZGdb as a resource for summaries of COI barcode data and metadata for important taxonomic groups of marine zooplankton and selected regions, including the North Atlantic, Arctic, North Pacific, and Southern Oceans. The MZGdb is designed to provide a foundation for analysis of species diversity of marine zooplankton based on DNA barcoding and metabarcoding for assessment of marine ecosystems and rapid detection of the impacts of climate change.

    

   more » « less
4. A modular plasmid toolkit applied in marine bacteria reveals functional insights during bacteria-stimulated metamorphosis

   https://doi.org/10.1128/mbio.01502-23  

   Alker, Amanda T. ; Farrell, Morgan V. ; Aspiras, Alpher E. ; Dunbar, Tiffany L. ; Fedoriouk, Andriy ; Jones, Jeffrey E. ; Mikhail, Sama R. ; Salcedo, Gabriella Y. ; Moore, Bradley S. ; Shikuma, Nicholas J. ( August 2023 , mBio)

   Ruby, Edward G. (Ed.)

   A conspicuous roadblock to studying marine bacteria for fundamental research and biotechnology is a lack of modular synthetic biology tools for their genetic manipulation. Here, we applied, and generated new parts for, a modular plasmid toolkit to study marine bacteria in the context of symbioses and host-microbe interactions. To demonstrate the utility of this plasmid system, we genetically manipulated the marine bacteriumPseudoalteromonas luteoviolacea, which stimulates the metamorphosis of the model tubeworm,Hydroides elegans. Using these tools, we quantified constitutive and native promoter expression, developed reporter strains that enable the imaging of host-bacteria interactions, and used CRISPR interference (CRISPRi) to knock down a secondary metabolite and a host-associated gene. We demonstrate the broader utility of this modular system for testing the genetic tractability of marine bacteria that are known to be associated with diverse host-microbe symbioses. These efforts resulted in the successful conjugation of 12 marine strains from the Alphaproteobacteria and Gammaproteobacteria classes. Altogether, the present study demonstrates how synthetic biology strategies enable the investigation of marine microbes and marine host-microbe symbioses with potential implications for environmental restoration and biotechnology.

   Marine Proteobacteria are attractive targets for genetic engineering due to their ability to produce a diversity of bioactive metabolites and their involvement in host-microbe symbioses. Modular cloning toolkits have become a standard for engineering model microbes, such asEscherichia coli, because they enable innumerable mix-and-match DNA assembly and engineering options. However, such modular tools have not yet been applied to most marine bacterial species. In this work, we adapt a modular plasmid toolkit for use in a set of 12 marine bacteria from the Gammaproteobacteria and Alphaproteobacteria classes. We demonstrate the utility of this genetic toolkit by engineering a marinePseudoalteromonasbacterium to study their association with its host animalHydroides elegans. This work provides a proof of concept that modular genetic tools can be applied to diverse marine bacteria to address basic science questions and for biotechnology innovations.

    

   more » « less
5. Finding needles in a haystack—Extensive diversity in the eustigmatophyceae revealed by community metabarcode analysis targeting the rbc L gene using lineage‐directed primers

   https://doi.org/10.1111/jpy.13196  

   Fawley, Marvin W. ; Fawley, Karen P. ; Cahoon, Aubrey Bruce ; Lane, ed., C. ( August 2021 , Journal of Phycology)

   Sequences from the Stramenopile class Eustigmatophyceae are rarely reported in metabarcoding studies, and when they have been reported, there are very few haplotypes. We hypothesized that the paucity of eustigmatophyte species detected in these studies may be a result of the metabarcoding techniques used, which have primarily employed universal ribosomal RNA gene regions. In this study, we examined environmental DNA samples from 22 sites in southwestern Virginia, some of which had previously been studied using ribosomal RNA analysis. We used metabarcoding techniques targeting the plastidrbcL gene with new primers designed to produce a 370 bp amplicon from all lineages of the Eustigmatophyceae in a reference collection. The amplicons were then analyzed with DADA2 to produce amplicon sequence variants (ASVs). Our results revealed 184rbcL haplotypes that can be tentatively assigned to the Eustigmatophyceae from these sites, representing much higher diversity than has been detected by ribosomal DNA‐based studies. The techniques employed can be used for future studies of population structure, ecology, distribution, and diversity of this class. With these techniques, it should be possible to make realistic estimates of the species‐level diversity of the Eustigmatophyceae on local, regional, and perhaps global scales.

    

   more » « less