{"corpus_id":2604491,"paper_sha":"76dd8dcaf2cabe41ae8a9081c6e937c871d174b4","doi":"10.1146/annurev-marine-010814-015902","arxiv_id":null,"pmid":25251272,"pmcid":null,"mag_id":2131510658,"dblp_id":null,"acl_id":null,"title":"Techniques for quantifying phytoplankton biodiversity.","year":2015,"publication_date":"2015-01-05","venue":"Annual Review of Marine Science","journal":{"name":"Annual review of marine science","pages":"\n          299-324\n        ","volume":"7"},"journal_issn":null,"journal_title":null,"publication_types":["Review","JournalArticle"],"pubmed_pub_types":["Journal Article","Research Support, U.S. Gov't, Non-P.H.S.","Review"],"s2_fields_of_study":["Biology","Medicine","Environmental Science"],"reference_count":127,"citation_count":40,"influential_citation_count":1,"is_open_access":true,"arxiv_categories":null,"arxiv_license":null,"arxiv_journal_ref":null,"mesh_headings":[{"d":"Biodiversity","mj":false,"ui":"D044822"},{"d":"Chromatography, High Pressure Liquid","mj":false,"ui":"D002851"},{"d":"DNA Fingerprinting","mj":false,"ui":"D016172"},{"d":"Ecosystem","mj":false,"ui":"D017753"},{"d":"Environmental Monitoring","mj":false,"qs":[{"q":"methods","mj":true,"ui":"Q000379"}],"ui":"D004784"},{"d":"Flow Cytometry","mj":false,"ui":"D005434"},{"d":"Gene Expression Profiling","mj":false,"ui":"D020869"},{"d":"In Situ Hybridization, Fluorescence","mj":false,"ui":"D017404"},{"d":"Metagenomics","mj":true,"ui":"D056186"},{"d":"Phylogeny","mj":false,"ui":"D010802"},{"d":"Phytoplankton","mj":true,"qs":[{"q":"cytology","mj":false,"ui":"Q000166"},{"q":"genetics","mj":false,"ui":"Q000235"},{"q":"metabolism","mj":false,"ui":"Q000378"}],"ui":"D010839"},{"d":"Proteomics","mj":true,"ui":"D040901"},{"d":"RNA, Ribosomal","mj":false,"qs":[{"q":"genetics","mj":false,"ui":"Q000235"}],"ui":"D012335"}],"chemicals":[{"n":"RNA, Ribosomal","ui":"D012335","reg":"0"}],"comments_corrections":null,"source_flags":5,"s2_open_access_pdf_url":"https://www.annualreviews.org/doi/pdf/10.1146/annurev-marine-010814-015902","s2_open_access_landing_url":"https://www.semanticscholar.org/paper/76dd8dcaf2cabe41ae8a9081c6e937c871d174b4","s2_open_access_license":"CCBY","s2_open_access_status":"HYBRID","pmc_open_access_pdf_url":null,"pmc_open_access_landing_url":null,"pmc_open_access_license":null,"pmc_open_access_status":null,"unpaywall_open_access_pdf_url":null,"unpaywall_open_access_landing_url":null,"unpaywall_open_access_license":null,"unpaywall_open_access_status":null,"abstract":"The biodiversity of phytoplankton is a core measurement of the state and activity of marine ecosystems. In the context of historical approaches, we review recent major advances in the technologies that have enabled deeper characterization of the biodiversity of phytoplankton. In particular, high-throughput sequencing of single loci/genes, genomes, and communities (metagenomics) has revealed exceptional phylogenetic and genomic diversity whose breadth is not fully constrained. Other molecular tools-such as fingerprinting, quantitative polymerase chain reaction, and fluorescence in situ hybridization-have provided additional insight into the dynamics of this diversity in the context of environmental variability. Techniques for characterizing the functional diversity of community structure through targeted or untargeted approaches based on RNA or protein have also greatly advanced. A wide range of techniques is now available for characterizing phytoplankton communities, and these tools will continue to advance through ongoing improvements in both technology and data interpretation.","claims":[{"public_id":"cl_e39c437dfcf56e39df31a161431e9b60","status":"active","text":"High-throughput sequencing of single loci/genes, genomes, and communities (metagenomics) has revealed exceptional phylogenetic and genomic diversity whose breadth is not fully constrained.","confidence":0.95,"contributors":[{"id":2,"public_id":"4715169a40","public_label":"AK (4715169a40)","roles":["extraction"],"url":"https://sah.borca.ai/u/4715169a40"},{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["review"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/claims/cl_e39c437dfcf56e39df31a161431e9b60"},{"public_id":"cl_6245a993d16da2932f824a04626ea8cb","status":"active","text":"Other molecular tools—such as fingerprinting, quantitative polymerase chain reaction, and fluorescence in situ hybridization—have provided additional insight into the dynamics of this diversity in the context of environmental variability.","confidence":0.9,"contributors":[{"id":2,"public_id":"4715169a40","public_label":"AK (4715169a40)","roles":["extraction"],"url":"https://sah.borca.ai/u/4715169a40"},{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["review"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/claims/cl_6245a993d16da2932f824a04626ea8cb"},{"public_id":"cl_7f924879bb23bc36da37b8b43fc0b9ca","status":"active","text":"Techniques for characterizing the functional diversity of community structure through targeted or untargeted approaches based on RNA or protein have also greatly advanced.","confidence":0.9,"contributors":[{"id":2,"public_id":"4715169a40","public_label":"AK (4715169a40)","roles":["extraction"],"url":"https://sah.borca.ai/u/4715169a40"},{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["review"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/claims/cl_7f924879bb23bc36da37b8b43fc0b9ca"}],"concepts":[{"public_id":"co_5d57931a523955fe36fa35120c7152db","status":"active","name":"functional diversity","description":"Characterization of community structure functional diversity through RNA- or protein-based approaches.","types":["measurement","finding"],"aliases":[],"contributors":[{"id":2,"public_id":"4715169a40","public_label":"AK (4715169a40)","roles":["extraction"],"url":"https://sah.borca.ai/u/4715169a40"},{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["review"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/concepts/co_5d57931a523955fe36fa35120c7152db"},{"public_id":"co_7ab11f17a98860338ad52671a0089a9a","status":"active","name":"fluorescence in situ hybridization","description":"A molecular tool (FISH) used to gain insight into phytoplankton diversity dynamics under environmental variability.","types":["method"],"aliases":["FISH"],"contributors":[{"id":2,"public_id":"4715169a40","public_label":"AK (4715169a40)","roles":["extraction"],"url":"https://sah.borca.ai/u/4715169a40"},{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["review"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/concepts/co_7ab11f17a98860338ad52671a0089a9a"},{"public_id":"co_859125082635d94cc20d686910c476b1","status":"active","name":"genomic diversity","description":"Exceptional breadth of genome-level variation revealed by high-throughput sequencing of phytoplankton.","types":["measurement","finding"],"aliases":[],"contributors":[{"id":2,"public_id":"4715169a40","public_label":"AK (4715169a40)","roles":["extraction"],"url":"https://sah.borca.ai/u/4715169a40"},{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["review"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/concepts/co_859125082635d94cc20d686910c476b1"},{"public_id":"co_987ad88a2d879a432246a0f04e4dd744","status":"active","name":"fingerprinting","description":"A molecular tool used to gain insight into phytoplankton diversity dynamics under environmental variability.","types":["method"],"aliases":[],"contributors":[{"id":2,"public_id":"4715169a40","public_label":"AK (4715169a40)","roles":["extraction"],"url":"https://sah.borca.ai/u/4715169a40"},{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["review"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/concepts/co_987ad88a2d879a432246a0f04e4dd744"},{"public_id":"co_c0b8e5ba37f5b954027962a7d85a2ab1","status":"active","name":"targeted approaches","description":"Approaches based on RNA or protein that target specific components to characterize functional diversity of phytoplankton community structure.","types":["method"],"aliases":[],"contributors":[{"id":2,"public_id":"4715169a40","public_label":"AK (4715169a40)","roles":["extraction"],"url":"https://sah.borca.ai/u/4715169a40"},{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["review"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/concepts/co_c0b8e5ba37f5b954027962a7d85a2ab1"},{"public_id":"co_f0f88051472a864bd50966f48690a771","status":"active","name":"quantitative polymerase chain reaction","description":"A molecular tool (qPCR) used to gain insight into phytoplankton diversity dynamics under environmental variability.","types":["method"],"aliases":["qPCR"],"contributors":[{"id":2,"public_id":"4715169a40","public_label":"AK (4715169a40)","roles":["extraction"],"url":"https://sah.borca.ai/u/4715169a40"},{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["review"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/concepts/co_f0f88051472a864bd50966f48690a771"},{"public_id":"co_fb9239ebbce0658e055abc89fd9b9783","status":"active","name":"phylogenetic diversity","description":"Exceptional breadth of evolutionary lineage diversity revealed by high-throughput sequencing of phytoplankton.","types":["measurement","finding"],"aliases":[],"contributors":[{"id":2,"public_id":"4715169a40","public_label":"AK (4715169a40)","roles":["extraction"],"url":"https://sah.borca.ai/u/4715169a40"},{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["review"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/concepts/co_fb9239ebbce0658e055abc89fd9b9783"},{"public_id":"co_fe26c56cce93daaf18d33a95d130c972","status":"active","name":"untargeted approaches","description":"Approaches based on RNA or protein that do not target specific components, used to characterize functional diversity of phytoplankton community structure.","types":["method"],"aliases":[],"contributors":[{"id":2,"public_id":"4715169a40","public_label":"AK (4715169a40)","roles":["extraction"],"url":"https://sah.borca.ai/u/4715169a40"},{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["review"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/concepts/co_fe26c56cce93daaf18d33a95d130c972"},{"public_id":"co_feba46e3fc4ccea4a1fc6716b9ce2cbd","status":"active","name":"high-throughput sequencing","description":"Sequencing methods that enable deep characterization of phytoplankton biodiversity, including single loci/genes, genomes, and metagenomics.","types":["method"],"aliases":["HTS"],"contributors":[{"id":2,"public_id":"4715169a40","public_label":"AK (4715169a40)","roles":["extraction"],"url":"https://sah.borca.ai/u/4715169a40"},{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["review"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/concepts/co_feba46e3fc4ccea4a1fc6716b9ce2cbd"}],"external_ids":{"DOI":"10.1146/annurev-marine-010814-015902","ArXiv":null,"PubMed":25251272,"PubMedCentral":null,"MAG":2131510658,"DBLP":null,"ACL":null},"open_access":{"is_open_access":true,"pdf_url":"https://www.annualreviews.org/doi/pdf/10.1146/annurev-marine-010814-015902","landing_url":"https://www.semanticscholar.org/paper/76dd8dcaf2cabe41ae8a9081c6e937c871d174b4","source":"semantic_scholar","pdf_url_source":"semantic_scholar_open_access_pdf","license":"CCBY","status":"HYBRID","reason":null},"reference_availability":{"status":"available","references_indexed":true,"full_text_available":false,"full_text_source":null,"count_basis":"semantic_scholar_metadata","extraction_status":"not_applicable","reason":null},"source":{"provider":"episteme2","base_corpus":"semantic_scholar_dump","freshness_mode":"unknown","basis":["semantic_scholar_metadata","postgres_metadata"],"limits":["paper metadata is based on indexed upstream scholarly datasets","claims and concepts are available only for extracted papers","absence of claims or concepts means no extracted graph data is available in this response"],"status":"available","degraded":false,"degraded_reasons":[],"diagnostics":{"status":"available","degraded":false,"degraded_reasons":[],"metadata_status":"available","graph_status":"available","abstract_status":"available"},"source_flags":5},"paper_id":632921,"paper_uid":"59d2ab92-a1a0-428a-a2fe-be7a0448c2e8","canonical_identity":{"paper_id":632921,"paper_uid":"59d2ab92-a1a0-428a-a2fe-be7a0448c2e8","identity_status":"available","lookup_basis":"semantic_scholar_external_id","compatibility_path":"corpus_id"},"url":"https://sah.borca.ai/papers/2604491"}