Multi‐Scale Spectroscopy to Map Intertidal Microbial Biofilm Community and Trait Diversity

ariela — Tue, 08 Jul 2025 23:11:00 +0000

Multi‐Scale Spectroscopy to Map Intertidal Microbial Biofilm Community and Trait Diversity ariela Tue, 07/08/2025 - 16:11

Document Category

Scientific Reports

Author(s)

Susan E. W. De la Cruz

Date

2025-06

Summary

Key Points:

We mapped intertidal microbial biofilm presence, quantity, diversity, and traits with spectroscopic data in San Francisco Bay, CA, USA
Maps revealed lipid, carbohydrate, and carbon concentrations 2 to 4 times greater in diatoms than in cyanobacteria and chlorophytes
This remote sensing approach enables greater understanding of biofilms' role in biogeochemical cycling, carbon budgets, and food webs

Abstract

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.

Plain Language Summary

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.

Citation:

Byrd, K. B., Palacios, S. L., Taylor, N. C., Woo, I., Moskal, S., Kokaly, R. F., et al. (2025). Multi‐scale spectroscopy to map
intertidal microbial biofilm community and trait diversity. Journal of Geophysical Research: Biogeosciences, 130, e2024JG008520. https://doi.org/10.1029/2024JG008520

Keywords

biofilm

mudflats

shorebird

Pond Complex

Eden Landing

Ravenswood

Content available here

JGR Biogeosciences article link