scholarly journals Digging for DNA at depth: rapid universal metabarcoding surveys (RUMS) as a tool to detect coral reef biodiversity across a depth gradient

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6379 ◽  
Author(s):  
Joseph D. DiBattista ◽  
James D. Reimer ◽  
Michael Stat ◽  
Giovanni D. Masucci ◽  
Piera Biondi ◽  
...  
Keyword(s):  
Coral Reef ◽  
Coral Reefs ◽  
Indicator Species ◽  
18S Rrna ◽  
Spatial Scales ◽  
Environmental Dna ◽  
Marine Biodiversity ◽  
Depth Gradient ◽  
Coral Reef Ecosystems ◽  
Eukaryotic Organisms

Background Effective biodiversity monitoring is fundamental in tracking changes in ecosystems as it relates to commercial, recreational, and conservation interests. Current approaches to survey coral reef ecosystems center on the use of indicator species and repeat surveying at specific sites. However, such approaches are often limited by the narrow snapshot of total marine biodiversity that they describe and are thus hindered in their ability to contribute to holistic ecosystem-based monitoring. In tandem, environmental DNA (eDNA) and next-generation sequencing metabarcoding methods provide a new opportunity to rapidly assess the presence of a broad spectrum of eukaryotic organisms within our oceans, ranging from microbes to macrofauna. Methods We here investigate the potential for rapid universal metabarcoding surveys (RUMS) of eDNA in sediment samples to provide snapshots of eukaryotic subtropical biodiversity along a depth gradient at two coral reefs in Okinawa, Japan based on 18S rRNA. Results Using 18S rRNA metabarcoding, we found that there were significant separations in eukaryotic community assemblages (at the family level) detected in sediments when compared across different depths ranging from 10 to 40 m (p = 0.001). Significant depth zonation was observed across operational taxonomic units assigned to the class Demospongiae (sponges), the most diverse class (contributing 81% of species) within the phylum Porifera; the oldest metazoan phylum on the planet. However, zonation was not observed across the class Anthozoa (i.e., anemones, stony corals, soft corals, and octocorals), suggesting that the former may serve as a better source of indicator species based on sampling over fine spatial scales and using this universal assay. Furthermore, despite their abundance on the examined coral reefs, we did not detect any octocoral DNA, which may be due to low cellular shedding rates, assay sensitivities, or primer biases. Discussion Overall, our pilot study demonstrates the importance of exploring depth effects in eDNA and suggest that RUMS may be applied to provide a baseline of information on eukaryotic marine taxa at coastal sites of economic and conservation importance.

scholarly journals ANALISIS STRATEGI PENGELOLAAN EKOSISTEM TERUMBU KARANG DI KAWASAN KONSERVASI PERAIRAN DAERAH LIUKANG TUPPABIRING

2020 ◽  
Vol 3 (2) ◽  
pp. 193-204
Author(s):  
Tenri A R ◽  
Danial Sultan ◽  
Asbar Asbar
Keyword(s):  
Coral Reef ◽  
Law Enforcement ◽  
Coral Reefs ◽  
Coral Cover ◽  
Strong Support ◽  
Marine Biodiversity ◽  
Prevention Measures ◽  
Eretmochelys Imbricata ◽  
Coral Reef Ecosystems ◽  
The Government

Liukang Tuppabiring is a waters with marine biodiversity potential large enough to be developed and managed sustainably. Utilization around the coral reefs in the waters of the Liukang Tuppabiring sub-district currently tends to lead to destructive use, so it is necessary to take damage prevention measures immediately. The results showed the condition of coral cover in the medium and damaged, while at stations 1,2,3,4,6 (25,47-41.07%), while conditions were good at station 5 (56.20%). The number of individual reef fish is 290 individuals from 46 species of 22 genera 11 families. At the research location also identified one type of protected biota namely Hawksbill (Eretmochelys imbricata). Coral damage that occurred at 6 observation stations was more caused by the practice of using destructive and environmentally unfriendly fishing equipment such as bombs, trawls, and the use of poisons. The priority strategies undertaken in the management of coral reefs at the study site are 1) Management of environmentally friendly coral reefs where the community as a manager with strong support from the Government; 2) Making clear rules related to utilization in coral reef areas and establishing a POSMAKWAS institution to avoid more severe coral damage; 3) Improve supervision and law enforcement must be firm in relation to the use of fishing gear that can damage coral reef ecosystems.

Regime shifts on tropical coral reef ecosystems: future trajectories to animal-dominated states in response to anthropogenic stressors

2021 ◽  
Author(s):  
James J. Bell ◽  
Valerio Micaroni ◽  
Francesca Strano
Keyword(s):  
Coral Reef ◽  
Coral Reefs ◽  
Regime Shift ◽  
Spatial Scales ◽  
Scleractinian Corals ◽  
Regime Shifts ◽  
Limited Information ◽  
Tropical Coral ◽  
Coral Reef Ecosystems ◽  
Tropical Coral Reef

Despite the global focus on the occurrence of regime shifts on shallow-water tropical coral reefs over the last two decades, most of this research continues to focus on changes to algal-dominated states. Here, we review recent reports (in approximately the last decade) of regime shifts to states dominated by animal groups other than zooxanthellate Scleractinian corals. We found that while there have been new reports of regime shifts to reefs dominated by Ascidacea, Porifera, Octocorallia, Zoantharia, Actiniaria and azooxanthellate Scleractinian corals, some of these changes occurred many decades ago, but have only just been reported in the literature. In most cases, these reports are over small to medium spatial scales (<4 × 104 m2 and 4 × 104 to 2 × 106 m2, respectively). Importantly, from the few studies where we were able to collect information on the persistence of the regime shifts, we determined that these non-scleractinian states are generally unstable, with further changes since the original regime shift. However, these changes were not generally back to coral dominance. While there has been some research to understand how sponge- and octocoral-dominated systems may function, there is still limited information on what ecosystem services have been disrupted or lost as a result of these shifts. Given that many coral reefs across the world are on the edge of tipping points due to increasing anthropogenic stress, we urgently need to understand the consequences of non-algal coral reef regime shifts.

scholarly journals Utilization of eDNA metabarcoding to assess coral reef health in Okinawa, Japan

2018 ◽  
Author(s):  
James D Reimer ◽  
Joseph DiBattista ◽  
Piera Biondi ◽  
Giovanni D Masucci ◽  
Michael Stat ◽  
...  
Keyword(s):  
Coral Reef ◽  
Environmental Dna ◽  
Global Scale ◽  
Coastal Development ◽  
Marine Biodiversity ◽  
Critical Data ◽  
Coral Reef Ecosystems ◽  
Reef Health ◽  
Seawater Samples ◽  
Over Exploitation

Environmental DNA (eDNA) metabarcoding has great potential in assessing comparative total biodiversity, and facilitating robust comparisons across a wide variety of sites and taxa. In particular, eDNA combined with next-generation sequencing can help address the huge critical data gaps in our understanding of marine biodiversity, especially in regions with high levels of understudied diversity such as the coral reefs of the Indo-Pacific region. Within this region, Okinawa is known for its high levels of marine biodiversity and endemicity, and also for the threats shallow coral reef ecosystems face from a variety of stressors including local-scale coastal development and over-exploitation to global scale threats such as climate change. In this study, we generated eDNA metabarcoding sequences from sediment and seawater samples from various reefs in Okinawa, Japan. At the same time, we developed a simple methodology to assess the relative health of these reefs based on anthropogenic and natural stressors. We discuss our eDNA results in comparison to coral reef health, identify potential bioindicator taxa, and explore the relative biodiversity of coral reef communities across sites. Our results indicate that taxa asides from the corals (Scleractinia) can provide robust information on coral reef health.

scholarly journals Utilization of eDNA metabarcoding to assess coral reef health in Okinawa, Japan

2018 ◽  
Author(s):  
James D Reimer ◽  
Joseph DiBattista ◽  
Piera Biondi ◽  
Giovanni D Masucci ◽  
Michael Stat ◽  
...  
Keyword(s):  
Coral Reef ◽  
Environmental Dna ◽  
Global Scale ◽  
Coastal Development ◽  
Marine Biodiversity ◽  
Critical Data ◽  
Coral Reef Ecosystems ◽  
Reef Health ◽  
Seawater Samples ◽  
Over Exploitation

Environmental DNA (eDNA) metabarcoding has great potential in assessing comparative total biodiversity, and facilitating robust comparisons across a wide variety of sites and taxa. In particular, eDNA combined with next-generation sequencing can help address the huge critical data gaps in our understanding of marine biodiversity, especially in regions with high levels of understudied diversity such as the coral reefs of the Indo-Pacific region. Within this region, Okinawa is known for its high levels of marine biodiversity and endemicity, and also for the threats shallow coral reef ecosystems face from a variety of stressors including local-scale coastal development and over-exploitation to global scale threats such as climate change. In this study, we generated eDNA metabarcoding sequences from sediment and seawater samples from various reefs in Okinawa, Japan. At the same time, we developed a simple methodology to assess the relative health of these reefs based on anthropogenic and natural stressors. We discuss our eDNA results in comparison to coral reef health, identify potential bioindicator taxa, and explore the relative biodiversity of coral reef communities across sites. Our results indicate that taxa asides from the corals (Scleractinia) can provide robust information on coral reef health.

KAJIAN PENGELOLAAN PESISIR DAN LAUT DENGAN SISTEM ZONASI DI KAWASAN KONSERVASI PERAIRAN DAERAH KECAMATAN LIUKANG TUPPABIRING

2021 ◽  
Vol 4 (1) ◽  
pp. 105-116
Author(s):  
Hamzah MS ◽  
Rustam Rustam ◽  
Abdul Rauf
Keyword(s):  
Coral Reef ◽  
Law Enforcement ◽  
Coral Reefs ◽  
Coral Cover ◽  
Strong Support ◽  
Marine Biodiversity ◽  
Prevention Measures ◽  
Eretmochelys Imbricata ◽  
Coral Reef Ecosystems ◽  
The Government

Liukang Tuppabiring is a waters with marine biodiversity potential large enough to be developed and managed sustainably. Utilization around the coral reefs in the waters of the Liukang Tuppabiring sub-district currently tends to lead to destructive use, so it is necessary to take damage prevention measures immediately. The results showed the condition of coral cover in the medium and damaged, while at stations 1,2,3,4,6 (25,47-41.07%), while conditions were good at station 5 (56.20%). The number of individual reef fish is 290 individuals from 46 species of 22 genera 11 families. At the research location also identified one type of protected biota namely Hawksbill (Eretmochelys imbricata). Coral damage that occurred at 6 observation stations was more caused by the practice of using destructive and environmentally unfriendly fishing equipment such as bombs, trawls, and the use of poisons. The priority strategies undertaken in the management of coral reefs at the study site are 1) Management of environmentally friendly coral reefs where the community as a manager with strong support from the Government; 2) Making clear rules related to utilization in coral reef areas and establishing a POSMAKWAS institution to avoid more severe coral damage; 3) Improve supervision and law enforcement must be firm in relation to the use of fishing gear that can damage coral reef ecosystems.

scholarly journals Spatial Scales of Bacterial Diversity in Cold-Water Coral Reef Ecosystems

PLoS ONE ◽  
2012 ◽  
Vol 7 (3) ◽  
pp. e32093 ◽  
Author(s):  
Sandra Schöttner ◽  
Christian Wild ◽  
Friederike Hoffmann ◽  
Antje Boetius ◽  
Alban Ramette
Keyword(s):  
Coral Reef ◽  
Bacterial Diversity ◽  
Cold Water ◽  
Spatial Scales ◽  
Coral Reef Ecosystems ◽  
Water Coral

scholarly journals Representative benthic habitat mapping on Lovina coral reefs in Northern Bali, Indonesia

2021 ◽  
Vol 22 (11) ◽  
Author(s):  
Anggita Kartikasari ◽  
TODHI PRISTIANTO ◽  
RIZKI HANINTYO ◽  
EGHBERT ELVAN AMPOU ◽  
TEJA ARIEF WIBAWA ◽  
...  
Keyword(s):  
Coral Reef ◽  
Coral Reefs ◽  
Habitat Mapping ◽  
Benthic Habitat ◽  
Coral Rubble ◽  
Spatial Coverage ◽  
Coral Reef Ecosystems ◽  
Optical Imagery ◽  
Sentinel 2

Abstract. Kartikasari A, Pristianto T, Hanintyo R, Ampou EE, Wibawa TA, Borneo BB. 2021. Representative benthic habitat mapping on Lovina coral reefs in Northern Bali, Indonesia. Biodiversitas 22: 4766-4774. Satellite optical imagery datasets integrated with in situ measurements are widely used to derive the spatial distribution of various benthic habitats in coral reef ecosystems. In this study, an approach to estimate spatial coverage of those habitats based on observation derived from Sentinel-2 optical imagery and a field survey, is presented. This study focused on the Lovina coral reef ecosystem of Northern Bali, Indonesia to support deployment of artificial reefs within the Indonesian Coral Reef Garden (ICRG) programme. Three specific locations were explored: Temukus, Tukad Mungga, and Baktiseraga waters. Spatial benthic habitat coverages of these three waters was estimated based on supervised classification techniques using 10m bands of Sentinel-2 imagery and the medium scale approach (MSA) transect method of in situ measurement.The study indicates that total coverage of benthic habitat is 61.34 ha, 25.17 ha, and 27.88 ha for Temukus, Tukad Mungga, and Baktiseraga waters, respectively. The dominant benthic habitat of those three waters consists of sand, seagrass, coral, rubble, reef slope and intertidal zone. The coral reef coverage is 29.48 ha (48%) for Temukus covered by genus Acropora, Isopora, Porites, Montipora, Pocillopora. The coverage for Tukad Mungga is 8.69 ha (35%) covered by genus Acropora, Montipora, Favia, Psammocora, Porites, and the coverage for Baktiseraga is 11.37 ha (41%) covered by genus Montipora sp, Goniastrea, Pavona, Platygyra, Pocillopora, Porites, Acropora, Leptoseris, Acropora, Pocillopora, Fungia. The results are expected to be suitable as supporting data in restoring coral reef ecosystems in the northern part of Bali, especially in Buleleng District.

scholarly journals Divergence of seafloor elevation and sea level rise in coral reef ecosystems

2017 ◽  
Vol 14 (6) ◽  
pp. 1739-1772 ◽  
Author(s):  
Kimberly K. Yates ◽  
David G. Zawada ◽  
Nathan A. Smiley ◽  
Ginger Tiling-Range
Keyword(s):  
Coral Reef ◽  
Coral Reefs ◽  
Sea Level Rise ◽  
Sea Level ◽  
Anthropogenic Impacts ◽  
Regional Scale ◽  
Coastal Hazards ◽  
Carbonate Production ◽  
Coral Reef Ecosystems ◽  
Study Sites

Abstract. Coral reefs serve as natural barriers that protect adjacent shorelines from coastal hazards such as storms, waves, and erosion. Projections indicate global degradation of coral reefs due to anthropogenic impacts and climate change will cause a transition to net erosion by mid-century. Here, we provide a comprehensive assessment of the combined effect of all of the processes affecting seafloor accretion and erosion by measuring changes in seafloor elevation and volume for five coral reef ecosystems in the Atlantic, Pacific, and Caribbean over the last several decades. Regional-scale mean elevation and volume losses were observed at all five study sites and in 77 % of the 60 individual habitats that we examined across all study sites. Mean seafloor elevation losses for whole coral reef ecosystems in our study ranged from −0.09 to −0.8 m, corresponding to net volume losses ranging from 3.4  ×  106 to 80.5  ×  106 m3 for all study sites. Erosion of both coral-dominated substrate and non-coral substrate suggests that the current rate of carbonate production is no longer sufficient to support net accretion of coral reefs or adjacent habitats. We show that regional-scale loss of seafloor elevation and volume has accelerated the rate of relative sea level rise in these regions. Current water depths have increased to levels not predicted until near the year 2100, placing these ecosystems and nearby communities at elevated and accelerating risk to coastal hazards. Our results set a new baseline for projecting future impacts to coastal communities resulting from degradation of coral reef systems and associated losses of natural and socioeconomic resources.

The scientific issues surrounding remote detection of submerged coral ecosystems

1998 ◽  
Vol 22 (2) ◽  
pp. 190-221 ◽  
Author(s):  
Heather Holden ◽  
Ellsworth LeDrew
Keyword(s):  
Remote Sensing ◽  
Coral Reef ◽  
Coral Reefs ◽  
Large Scale ◽  
Aerial Photographs ◽  
Coastal Zones ◽  
Global Status ◽  
Coral Reef Ecosystems ◽  
Remote Estimation

According to the 1993 colloquium on the ‘Global status of coral reefs', our understanding of the global role of coral reefs is inadequate. To increase our understanding, an accurate large-scale mapping and monitoring programme is necessary. Historically, coastal zones have been mapped using traditional surveying tools such as topographic maps, nautical charts, existing aerial photographs and direct observations. Although less expensive than digital imagery, exclusive use of these traditional tools may not be practical for monitoring large or remote coral reef ecosystems accurately. Researchers are attempting to develop an adequate coral reef mapping system based on digital remote sensing, but are impeded by issues such as effects of the intervening water column and spectral distinction of bottom types. The two variables discussed, which will contribute to our understanding of the global role of coral reefs, are: 1) remote sensing of submerged coral reefs in general; and 2) remote sensing of coral bleaching in particular. A summary of radiative transfer theory is presented and case studies of attempts at mapping remotely the geographic extent and health of submerged ecosystems, as well as a discussion of the remote estimation of water depth and quality. Problems in the translation and delivery of information to the end user are presented, and possible solutions suggested.

Mapping coral reef environments

2017 ◽  
Vol 41 (6) ◽  
pp. 803-833 ◽  
Author(s):  
Sarah M. Hamylton
Keyword(s):  
Coral Reef ◽  
Coral Reefs ◽  
Environmental Drivers ◽  
Marine Biodiversity ◽  
Management Tools ◽  
Breeding Sites ◽  
Recent Advances ◽  
Reef Environments ◽  
Aerial Vehicle ◽  
Historical Methods

Coral reef environments support high levels of marine biodiversity, they are important sites for coastal habitation and they provide a range of goods and ecosystem services such as nearshore fisheries, economic revenue from tourism and breeding sites for seabirds and turtles. Mapping is a fundamental activity that underpins our understanding of coral reef environments and helps to shape policies in resource management and conservation. This is particularly the case for quantifying the area of landcover types associated with reef environments, including coral patches, seagrasses and mangroves, but also for monitoring how these change over time and modelling how spatial patterns apparent on reefs are related to environmental drivers. Field techniques and aerial photography have historically played a crucial role in mapping coral reef environments, which has recently seen a transition toward the processing of satellite remote sensing images. This paper examines a series of maps produced of Low Isles, the most mapped island on the Great Barrier Reef, to review historical methods for mapping coral reefs because of the critical importance of understanding how past maps were made, which determines appropriate uses to which they can be put. Recent advances and future opportunities for the application of mapping technologies to coral reefs are also evaluated, including the use of unmanned aerial vehicle (UAV) platforms for airborne surveys, delivery of information through web-based platforms and improvements in the quality of information for making and presenting maps. Maps have transformed the way we have responded to both historic and contemporary coral reef problems. This timely review communicates how maps, and the fast growing technologies that are employed to produce them, are central to our understanding of coral reef environments. Recent advances that may drive exciting new environmental management tools are identified.

Sign in / Sign up

Export Citation Format

Share Document