Niky Taylor https://www.southbayrestoration.org/ en Multi‐Scale Spectroscopy to Map Intertidal Microbial Biofilm Community and Trait Diversity https://www.southbayrestoration.org/document/multi-scale-spectroscopy-map-intertidal-microbial-biofilm-community-and-trait-diversity <span class="field field--name-title field--type-string field--label-hidden">Multi‐Scale Spectroscopy to Map Intertidal Microbial Biofilm Community and Trait Diversity</span> <span class="field field--name-uid field--type-entity-reference field--label-hidden"><span>ariela</span></span> <span class="field field--name-created field--type-created field--label-hidden">Tue, 07/08/2025 - 16:11</span> <div class="field field--name-field-document-category field--type-entity-reference field--label-above"> <div class="field__label">Document Category</div> <div class="field__items"> <div class="field__item">Scientific Reports</div> </div> </div> <div class="field field--name-field-author field--type-entity-reference field--label-above"> <div class="field__label">Author(s)</div> <div class="field__items"> <div class="field__item"><a href="/authors/kristin-byrd" hreflang="en">Kristin Byrd</a></div> <div class="field__item"><a href="/authors/sherry-palacios" hreflang="en">Sherry Palacios</a></div> <div class="field__item"><a href="/authors/niky-taylor" hreflang="en">Niky Taylor</a></div> <div class="field__item"><a href="/authors/isa-woo" hreflang="en">Isa Woo</a></div> <div class="field__item"><a href="/authors/stacy-m-moskal-0" hreflang="en">Stacy M. Moskal</a></div> <div class="field__item"><a href="/authors/raymond-kokaly" hreflang="en">Raymond Kokaly</a></div> <div class="field__item"><a href="/authors/todd-hoefen" hreflang="en">Todd Hoefen</a></div> <div class="field__item"><a href="/authors/john-chapman" hreflang="en">John Chapman</a></div> <div class="field__item"><a href="/authors/susan-e-w-de-la-cruz" hreflang="en">Susan E. W. De la Cruz</a></div> </div> </div> <div class="field field--name-field-date-document field--type-string field--label-above"> <div class="field__label">Date</div> <div class="field__item">2025-06</div> </div> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-above"> <div class="field__label">Summary</div> <div class="field__item"><h2>Key Points:</h2><ul><li>We mapped intertidal microbial biofilm presence, quantity, diversity, and traits with spectroscopic data in San Francisco Bay, CA, USA</li><li>Maps revealed lipid, carbohydrate, and carbon concentrations 2 to 4 times greater in diatoms than in cyanobacteria and chlorophytes</li><li>This remote sensing approach enables greater understanding of biofilms' role in biogeochemical cycling, carbon budgets, and food webs</li></ul><h2>Abstract </h2><p>Intertidal microbial biofilms, or microphytobenthos, support estuarine biogeochemical cycling, the physical stability of mudflats, and food webs, particularly those of migratory shorebirds. Photosynthetic biofilms dominated by diatoms, cyanobacteria, and chlorophytes represent a significant fraction of biofilm biomass and contain pigments that can be detected with remote sensing. These diverse biofilm community types vary in indicator pigments and functional traits related to biogeochemical cycling and nutritional quality. We modeled and mapped spatial variation in intertidal biofilm distribution, quantity, diversity, and functional traits using multi‐scale spectroscopic data collected within southern San Francisco Bay, California, USA (South SFB). We developed a new biofilm index (B‐index) from 5 mm HySpex spectra to detect biofilm presence. We developed single and multiple response partial least squares regression (PLS) models of chlorophyll‐a (chl‐a; biomass indicator), indicator pigments: fucoxanthin and diadinoxanthin (diatoms), zeaxanthin (cyanobacteria), and chl‐b (chlorophytes), and functional traits: carbohydrates, lipids, and total organic carbon from paired in situ biofilm data and field spectra. The B‐index and PLS models were scaled to South SFB with a 3.7m AVIRIS‐NG hyperspectral image. The model %RMSE calculated from AVIRIS‐NG test samples ranged from 12.7% for chla to 49% for chl‐b; for six of the eight models, %RMSE was 23% or below. Mapped community types differed in mapped traits, with average lipid concentrations three times higher in areas indicated as diatoms compared to other groups. Available maps depict for the first time the spatial variation of an important shorebird food resource and inform the contribution of intertidal biofilm in carbon and nutrient cycling.</p><h2>Plain Language Summary</h2><p>Microbial biofilm communities grow on the surface of intertidal mudflats. Biofilms contribute to estuarine biogeochemical cycling and migratory shorebird food webs. Sampling biofilm in mudflats is challenging, yet most biofilms contain pigments that enable them to be detected with remote sensing. We used spectroscopy, the measurement of contiguous swaths of spectra in the visible to shortwave infrared wavelengths, to model and map intertidal biofilm presence, quantity, diversity, and functional traits in southern San Francisco Bay, California, USA. We developed a new index with 5‐mm fieldbased HySpex spectra to detect biofilm presence. We mapped diatom, cyanobacteria, and chlorophyte community types based on indicator pigments, and biomass and carbohydrate, lipid, and total organic carbon nutritional traits using a 3.7‐m AVIRIS‐NG airborne imaging spectrometer image. We created maps by applying partial least squares regression models of paired biofilm‐field spectral data collected over 2 years. Concentrations of mapped nutritional traits were two to four time greater in the mapped diatoms than in mapped cyanobacteria or chlorophytes. This remote sensing approach produced for the first time the distribution of an important migratory shorebird food resource. The approach will also help improve our understanding of the role of intertidal biofilms in carbon and nutrient cycling.</p><h2>Citation:</h2><p>Byrd, K. B., Palacios, S. L., Taylor, N. C., Woo, I., Moskal, S., Kokaly, R. F., et al. (2025). Multi‐scale spectroscopy to map<br />intertidal microbial biofilm community and trait diversity. Journal of Geophysical Research: Biogeosciences, 130, e2024JG008520. <a href="https://doi.org/10.1029/2024JG008520">https://doi.org/10.1029/2024JG008520</a></p><p> </p></div> </div> <div class="field field--name-field-keywords field--type-entity-reference field--label-above"> <div class="field__label">Keywords</div> <div class="field__items"> <div class="field__item"><a href="/taxonomy/term/1042" hreflang="en">biofilm</a></div> <div class="field__item"><a href="/keywords/mudflats" hreflang="en">mudflats</a></div> <div class="field__item"><a href="/taxonomy/term/958" hreflang="en">shorebird</a></div> </div> </div> <div class="field field--name-field-pond-complex field--type-entity-reference field--label-above"> <div class="field__label">Pond Complex</div> <div class="field__items"> <div class="field__item"><div id="taxonomy-term-55" class="taxonomy-term vocabulary-pond-complex"> <h2><a href="/taxonomy/term/55"> <div class="field field--name-name field--type-string field--label-hidden field__item"><a href="/taxonomy/term/55" hreflang="en">Eden Landing</a></div> </a></h2> <div class="content"> <div class="layout layout--twocol-section layout--twocol-section--25-75"> <div class="layout__region layout__region--first"> <div class="block block-layout-builder block-field-blocktaxonomy-termpond-complexfield-pond-complex-image"> <div class="field field--name-field-pond-complex-image field--type-image field--label-hidden field__items"> <div class="field__item"> <a href="/taxonomy/term/55" hreflang="en"><img loading="lazy" src="/sites/default/files/styles/thumbnail_50x50_/public/2019-05/EdenLandingMaps.png?itok=Ul4jIguL" width="50" height="50" alt="Eden Landing Map" class="image-style-thumbnail-50x50-" /> </a> </div> </div> </div> </div> <div class="layout__region layout__region--second"> <div class="block block-layout-builder block-field-blocktaxonomy-termpond-complexname"> <div class="field field--name-name field--type-string field--label-hidden field__item"><a href="/taxonomy/term/55" hreflang="en">Eden Landing</a></div> </div> </div> </div> </div> </div> </div> <div class="field__item"><div id="taxonomy-term-54" class="taxonomy-term vocabulary-pond-complex"> <h2><a href="/taxonomy/term/54"> <div class="field field--name-name field--type-string field--label-hidden field__item"><a href="/taxonomy/term/54" hreflang="en">Ravenswood</a></div> </a></h2> <div class="content"> <div class="layout layout--twocol-section layout--twocol-section--25-75"> <div class="layout__region layout__region--first"> <div class="block block-layout-builder block-field-blocktaxonomy-termpond-complexfield-pond-complex-image"> <div class="field field--name-field-pond-complex-image field--type-image field--label-hidden field__items"> <div class="field__item"> <a href="/taxonomy/term/54" hreflang="en"><img loading="lazy" src="/sites/default/files/styles/thumbnail_50x50_/public/2019-05/ravenswood.png?itok=FYrqWj3J" width="50" height="50" alt="Ravenswood map" class="image-style-thumbnail-50x50-" /> </a> </div> </div> </div> </div> <div class="layout__region layout__region--second"> <div class="block block-layout-builder block-field-blocktaxonomy-termpond-complexname"> <div class="field field--name-name field--type-string field--label-hidden field__item"><a href="/taxonomy/term/54" hreflang="en">Ravenswood</a></div> </div> </div> </div> </div> </div> </div> </div> </div> <div class="field field--name-field-website-link field--type-link field--label-above"> <div class="field__label">Content available here</div> <div class="field__item"><a href="https://agupubs.onlinelibrary.wiley.com/doi/10.1029/2024JG008520" target="_blank">JGR Biogeosciences article link</a></div> </div> Tue, 08 Jul 2025 23:11:00 +0000 ariela 2567 at https://www.southbayrestoration.org