Dataset Information

Genome of a novel Sediminibacterium discovered in association with two species of freshwater cyanobacteria from streams in Southern California.

ABSTRACT: Here, we report the discovery of a novel Sediminibacterium sequenced from laboratory cultures of freshwater stream cyanobacteria from sites in Southern California, grown in BG11 medium. Our genome-wide analyses reveal a highly contiguous and complete genome (97% BUSCO) that is placed within sediminibacterial clades in phylogenomic analyses. Functional annotation indicates the presence of genes that could be involved in mutualistic/commensal relationship with associated cyanobacterial hosts.

SUBMITTER: Sethuraman A

PROVIDER: S-EPMC9258536 | biostudies-literature | 2022 Jul

REPOSITORIES: biostudies-literature

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Genome of a novel Sediminibacterium discovered in association with two species of freshwater cyanobacteria from streams in Southern California.

Sethuraman Arun A Stancheva Rosalina R Sanders Ciara C Caceres Lakme L Castro David D Hausknecht-Buss Hannah H Henry Simone S Johansen Haven H Kasler Antolette A Lastor Sandy S Massaro Isabelle I Mekuria Immanuel I Moron-Solano Andrea A Read Niki N Vengerova Gretchen G Zhang Andrew A Zhang Xiaoyu X Read Betsy B

G3 (Bethesda, Md.) 20220701 7

Here, we report the discovery of a novel Sediminibacterium sequenced from laboratory cultures of freshwater stream cyanobacteria from sites in Southern California, grown in BG11 medium. Our genome-wide analyses reveal a highly contiguous and complete genome (97% BUSCO) that is placed within sediminibacterial clades in phylogenomic analyses. Functional annotation indicates the presence of genes that could be involved in mutualistic/commensal relationship with associated cyanobacterial hosts. ...[more]

PMID: 35639673

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Project description:The ranges and abundances of species that depend on freshwater habitats are declining worldwide. Efforts to counteract those trends are often hampered by a lack of information about species distribution and conservation status and are often strongly biased toward a few well-studied groups. We identified the 3,906 vascular plants, macroinvertebrates, and vertebrates native to California, USA, that depend on fresh water for at least one stage of their life history. We evaluated the conservation status for these taxa using existing government and non-governmental organization assessments (e.g., endangered species act, NatureServe), created a spatial database of locality observations or distribution information from ~400 data sources, and mapped patterns of richness, endemism, and vulnerability. Although nearly half of all taxa with conservation status (n = 1,939) are vulnerable to extinction, only 114 (6%) of those vulnerable taxa have a legal mandate for protection in the form of formal inclusion on a state or federal endangered species list. Endemic taxa are at greater risk than non-endemics, with 90% of the 927 endemic taxa vulnerable to extinction. Records with spatial data were available for a total of 2,276 species (61%). The patterns of species richness differ depending on the taxonomic group analyzed, but are similar across taxonomic level. No particular taxonomic group represents an umbrella for all species, but hotspots of high richness for listed species cover 40% of the hotspots for all other species and 58% of the hotspots for vulnerable freshwater species. By mapping freshwater species hotspots we show locations that represent the top priority for conservation action in the state. This study identifies opportunities to fill gaps in the evaluation of conservation status for freshwater taxa in California, to address the lack of occurrence information for nearly 40% of freshwater taxa and nearly 40% of watersheds in the state, and to implement adequate protections for freshwater taxa where they are currently lacking.

Project description:Invasive species are a widespread threat to stream ecosystems across the planet. In Southern California, USA, the invasive red swamp crayfish Procambarus clarkii (Girard, 1852) poses a significant threat to native aquatic fauna. Studies have suggested that artificial refuge traps (ARTs) resembling crayfish burrows can be used to remove invasive crayfish, but, to date, no studies have focused on optimizing ART design and deployment to maximize crayfish catch. This month-long study tested the effect of modifications on ART diameter, color, and soak time on P. clarkii catch effectiveness across 160 traps. We evaluated catch data by creating multiple candidate generalized linear mixed models predicting P. clarkii catches with different modeling parameterizations and a priori hypothesized predictor variables. During the study period, ARTs removed a total of 240 red swamp crayfish with no incidental bycatch. Larger P. clarkii (2-6-cm carapace length) were found more frequently in 5.1-cm-diameter traps, and smaller P. clarkii (1-4 cm) were found more frequently in 2.5-cm-diameter traps. Catch numbers varied between trap types, with black-colored 5.1-cm-diameter traps removing the greatest amount of the total P. clarkii caught in the study (mean = 0.27, SD = 0.29; 35% of the total caught) and black-colored 2.5-cm-diameter traps removing the least amount (mean = 0.09, SD = 0.55; 12% of the total). Further, ART deployment duration was an important predictor variable for candidate models, where ARTs with 4-d and 7-d deployment durations had lower catch/unit effort than traps with 1-d and 2-d deployments. This factorial experiment is the 1st study to suggest specific design modifications to ARTs that optimize invasive red swamp crayfish removal without incurring non-target incidental bycatch. This study demonstrates that ARTs can be a valuable tool for conservation managers interested in restoring streams through invasive crayfish removal, especially where there are sensitive biological resources.

Dataset Information

Genome of a novel Sediminibacterium discovered in association with two species of freshwater cyanobacteria from streams in Southern California.

Publications

Genome of a novel Sediminibacterium discovered in association with two species of freshwater cyanobacteria from streams in Southern California.

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