The habitat-modifying red alga Ramicrusta on Pacific reefs: A new generic record for the Tropical Northwestern Pacific and the description of four new species from Guam

Mills, Matthew S.; Schils, Tom

doi:10.1371/journal.pone.0259336

Cited by 8 publications

(18 citation statements)

References 40 publications

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“…The mitochondrial cytochrome c oxidase subunit I, COI-5P (roughly 664 bp), is a barcode marker that is regularly used for DNA barcoding of red algae [55] and was used for both the Corallinales and Peyssonneliales. The primer combination used to amplify COI-5P was TS_COI_F01_10 (5'-TCGARTCYCGTCTCTCTCG-3') [56] and the reverse primer, GWSRx [57]. Protocols for COI-5P amplification follow Mills & Schils [56].…”

Section: Plos Onementioning

confidence: 99%

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Community assessment of crustose calcifying red algae as coral recruitment substrates

Deinhart

Mills²,

Schils³

2022

PLoS ONE

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Successful recruitment of invertebrate larvae to reef substrates is essential to the health of tropical coral reef ecosystems and to their capacity to recover from disturbances. Crustose calcifying red algae (CCRA) are a species rich group of seaweeds that have been identified as important recruitment substrates for scleractinian corals. Most studies on the settlement preference of coral larvae on CCRA use morphological species identifications that can lead to unreliable species identification and do not allow for examining species-specific interactions between coral larvae and CCRA. Accurate identifications of CCRA species is important for coral reef restoration and management to assess CCRA community composition and to detect CCRA species that are favored as coral recruitment substrates. In this study, DNA sequence analysis, was used to identify CCRA species to (1) investigate the species richness and community composition of CCRA on experimental coral recruitment tiles and (2) assess if the coral Acropora surculosa preferred any of these CCRA species as recruitment substrates. The CCRA community assemblages on the coral recruitment tiles was species-rich, comprising 27 distinct CCRA species of the orders Corallinales and Peyssonneliales which constitute new species records for Guam. Lithophylloideae sp. 1 (Corallinales) was the CCRA species that was significantly favored by coral larvae as a recruitment substrate. Lithophylloideae sp. 1 showed to hold a valuable ecological role for coral larval recruitment preference. Lithophylloideae sp. 1 had the highest benthic cover on the recruitment tiles and contained most A. surculosa recruits. DNA barcoding revealed a high taxonomic diversity of CCRA species on a microhabitat scale and provided detailed insight into the species-specific ecological interactions between CCRA and corals. With a steady decline in coral cover, detailed information on species interactions that drive reef recovery is valuable for the planning of marine management actions and restoration efforts.

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Section: Plos Onementioning

confidence: 99%

“…The primer combination used to amplify COI-5P was TS_COI_F01_10 (5'-TCGARTCYCGTCTCTCTCG-3') [56] and the reverse primer, GWSRx [57]. Protocols for COI-5P amplification follow Mills & Schils [56].…”

Section: Plos Onementioning

confidence: 99%

Community assessment of crustose calcifying red algae as coral recruitment substrates

Deinhart

Mills²,

Schils³

2022

PLoS ONE

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Section: Discussionmentioning

confidence: 76%

“…Of the 154 species found in this study, only ten of them matched (≥ 98% COI-5P similarity) sequences of described species, four of those were only described from Guam last year (Mills and Schils, 2021), suggesting that many of these CCRA species are possibly new to science. These findings are also consistent with recent studies that revealed extensive degrees of endemism and cryptic diversity within Guam's seaweed flora (Verbruggen and Schils, 2012;Gabriel et al, 2017;Leliaert et al, 2018;Gabriel et al, 2019;Mills and Schils, 2021;Vieira et al, 2022). Additionally, the CCRA diversity reported herein is greater than those of much larger coastal and oceanic ecosystems, including those documented in recent studies in New Zealand and Brazil (Twist et al, 2019;Sissini et al, 2021), in other barcoding blitzes in Hawaii, Taiwan, Tunisia, and…”

Section: Discussionmentioning

confidence: 76%

“…Therefore, different primer combinations were tested to amplify COI-5P for every specimen. The primers used include GWSFn and GWSRx, the primers utilized by Saunders and McDevit (2012), as well as TS_COI_F01_10 (Mills and Schils, 2021). COI-5P was amplified following the amplification profile 95°C for 3 minutes; 35 cycles of 94°C for 40 seconds, annealing at 48°C for 40 seconds, extension at 72°C for 1:40 minutes; and a final extension at 72°C for 10 minutes.…”

Section: Polymerase Chain Reaction (Pcr)mentioning

confidence: 99%

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Small tropical islands as hotspots of crustose calcifying red algal diversity and endemism

et al. 2022

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In the tropics, crustose calcifying red algae (Corallinophycidae and Peyssonneliales; CCRA) are dominant and important reef builders that serve a suite of ecological functions affecting reef health. However, CCRA taxa have historically been overlooked in floristic and ecological studies because of their high degrees of phenotypic plasticity and morphological convergence that impede reliable identifications based on morphology. This study provides an update of the CCRA diversity of Guam (Mariana Islands) based on a recent DNA barcoding effort. This account of CCRA taxa is compared to (1) the most current species inventories for Guam based on morphological identifications and (2) similar floristic accounts of CCRA from other regions using DNA barcoding. 492 CCRA specimens were collected from Guam for which two markers, COI-5P and psbA, were used for phylogenetic analysis and species delimitation. Phylogenetic relationships were inferred using maximum likelihood. Species richness estimates were obtained through a conservative approach using the Automatic Barcode Gap Discovery method for species delimitation. A total of 154 putative CCRA species were identified, with 106 representatives of the subclass Corallinophycidae and 48 belonging to the order Peyssonneliales. When compared to previous studies based on morphological identification, molecular data suggests that all but one of the CCRA species reported for Guam were incorrectly identified and CCRA species richness is more than six times higher than previously assumed. Species accumulation curves show that CCRA species richness will continue to rise with increased sampling effort and the exploration of new (micro)habitats before reaching a plateau. Guam’s true CCRA richness might eventually exceed the currently reported species richness of all marine red algae for the island. Of the 154 putative species documented in this study, only ten closely match (≥ 98% COI-5P sequence similarity) previously described species, implying that many are probably new species to science. The here-reported CCRA diversity for Guam as a small, remote tropical island in the Western Pacific Ocean is greater than those of well-documented CCRA floras for much larger nearshore ecosystems in Brazil and New Zealand, emphasizing the value of tropical islands as hotspots of marine biodiversity.

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Assessment of the utility of underwater hyperspectral imaging for surveying and monitoring coral reef ecosystems

Mills,

Ungermann,

Rigot

et al. 2023

Sci Rep

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Technological innovations that improve the speed, scale, reproducibility, and accuracy of monitoring surveys will allow for a better understanding of the global decline in tropical reef health. The DiveRay, a diver-operated hyperspectral imager, and a complementary machine learning pipeline to automate the analysis of hyperspectral imagery were developed for this purpose. To evaluate the use of a hyperspectral imager underwater, the automated classification of benthic taxa in reef communities was tested. Eight reefs in Guam were surveyed and two approaches for benthic classification were employed: high taxonomic resolution categories and broad benthic categories. The results from the DiveRay surveys were validated against data from concurrently conducted photoquadrat surveys to determine their accuracy and utility as a proxy for reef surveys. The high taxonomic resolution classifications did not reliably predict benthic communities when compared to those obtained by standard photoquadrat analysis. At the level of broad benthic categories, however, the hyperspectral results were comparable to those of the photoquadrat analysis. This was particularly true when estimating scleractinian coral cover, which was accurately predicted for six out of the eight sites. The annotation libraries generated for this study were insufficient to train the model to fully account for the high biodiversity on Guam’s reefs. As such, prediction accuracy is expected to improve with additional surveying and image annotation. This study is the first to directly compare the results from underwater hyperspectral scanning with those from traditional photoquadrat survey techniques across multiple sites with two levels of identification resolution and different degrees of certainty. Our findings show that dependent on a well-annotated library, underwater hyperspectral imaging can be used to quickly, repeatedly, and accurately monitor and map dynamic benthic communities on tropical reefs using broad benthic categories.

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The habitat-modifying red alga Ramicrusta on Pacific reefs: A new generic record for the Tropical Northwestern Pacific and the description of four new species from Guam

Cited by 8 publications

References 40 publications

Community assessment of crustose calcifying red algae as coral recruitment substrates

Community assessment of crustose calcifying red algae as coral recruitment substrates

Small tropical islands as hotspots of crustose calcifying red algal diversity and endemism

Assessment of the utility of underwater hyperspectral imaging for surveying and monitoring coral reef ecosystems

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