SoxY gene family expansion underpins adaptation to diverse hosts and environments in symbiotic sulfide oxidizers.

Sulfur-oxidizing bacteria (SOB) have developed distinct ecological strategies to obtain reduced sulfur compounds for growth. These range from specialists that can only use a limited range of reduced sulfur compounds to generalists that can use many different forms as electron donors. Forming intimate symbioses with animal hosts is another highly successful ecological strategy for SOB, as animals, through their behavior and physiology, can enable access to sulfur compounds. Symbioses have evolved multiple times in a range of animal hosts and from several lineages of SOB. They have successfully colonized a wide range of habitats, from seagrass beds to hydrothermal vents, with varying availability of symbiont energy sources. Our extensive analyses of sulfur transformation pathways in 234 genomes of symbiotic and free-living SOB revealed widespread conservation in metabolic pathways for sulfur oxidation in symbionts from different host species and environments, raising the question of how they have adapted to such a wide range of distinct habitats. We discovered a gene family expansion of soxY in these genomes, with up to five distinct copies per genome. Symbionts harboring only the "canonical" soxY were typically ecological "specialists" that are associated with specific host subfamilies or environments (e.g., hydrothermal vents, mangroves). Conversely, symbionts with multiple divergent soxY genes formed versatile associations across diverse hosts in various marine environments. We hypothesize that expansion and diversification of the soxY gene family could be one genomic mechanism supporting the metabolic flexibility of symbiotic SOB enabling them and their hosts to thrive in a range of different and dynamic environments.IMPORTANCESulfur metabolism is thought to be one of the most ancient mechanisms for energy generation in microorganisms. A diverse range of microorganisms today rely on sulfur oxidation for their metabolism. They can be free-living, or they can live in symbiosis with animal hosts, where they power entire ecosystems in the absence of light, such as in the deep sea. In the millions of years since they evolved, sulfur-oxidizing bacteria have adopted several highly successful strategies; some are ecological "specialists," and some are "generalists," but which genetic features underpin these ecological strategies are not well understood. We discovered a gene family that has become expanded in those species that also seem to be "generalists," revealing that duplication, repurposing, and reshuffling existing genes can be a powerful mechanism driving ecological lifestyle shifts.

National assessment and variability of blue carbon in seagrass ecosystems in Thailand.

Seagrass ecosystems are important organic carbon (Corg) sinks with great potential to contribute to climate change mitigation strategies. However, the high spatial and temporal variability is a barrier to the accurate assessment of national Corg stocks. This study provides a national assessment of Corg within seagrass meadows, including spatial and temporal variations. The highest Corg stocks were within mangrove-associated (44.3 ± 8.27 Mg ha-1), while near-surface sediments were highest in reef-associated meadows (10.20 ± 3.69 Mg ha-1). Regionally, the highest stocks were in the Upper Andaman coast in monospecific meadows (51.7 ± 7.14 Mg ha-1). Corg stocks in near-surface sediments were significantly different across historical trends (p < 0.001), with the highest stocks in stable meadows (9.28 ± 3.39 Mg ha-1). The national Corg stock within seagrass meadows sediment was 40.45 ± 11.59 Mg C ha-1. The results of this study highlighted the complexity of blue carbon in seagrass meadows and the associated impacts on national Corg assessments, carbon accounting, and conservation strategies.

Blue carbon assessments of seagrass and mangrove ecosystems in South and Southeast Asia: Current progress and knowledge gaps.

Coastal blue carbon ecosystems can be an important nature-based solution for mitigating climate change, when emphasis is given to their protection, management, and restoration. Globally, there has been a rapid increase in blue carbon research in the last few decades, with substantial investments on national scales by the European Union, the USA, Australia, Seychelles, and Belize. Blue carbon ecosystems in South and Southeast Asia are globally diverse, highly productive and could represent a global hotspot for carbon sequestration and storage. To guide future efforts, we conducted a systematic review of the available literature on two primary blue carbon ecosystems-seagrasses and mangroves-across 13 countries in South and Southeast Asia to assess existing national inventories, review current research trends and methodologies, and identify existing knowledge gaps. Information related to various aspects of seagrass and mangrove ecosystems was extracted from 432 research articles from 1967 to 2022. We find that: (1) blue carbon estimates in several countries have limited data, especially for seagrass meadows compared to mangrove ecosystems, although the highest reported carbon stocks were in Indonesia and the Philippines with 4,515 and 707 Tg within mangrove forest and 60.9 and 63.3 Tg within seagrass meadows, respectively; (2) there is a high difference in the quantity and quality of data between mangrove and seagrass ecosystems, and the methodologies used for blue carbon estimates are highly variable across countries; and (3) most studies on blue carbon stocks are spatially biased towards more familiar study areas of individual countries, than several lesser-known suspected blue carbon hotspots. In sum, our review demonstrates the paucity and variability in current research in the region, and highlights research frontiers that should be addressed by future research before the robust implementation of these ecosystems into national climate strategies.

Quantification of blue carbon in seagrass ecosystems of Southeast Asia and their potential for climate change mitigation.

Seagrasses have the ability to contribute towards climate change mitigation, through large organic carbon (Corg) sinks within their ecosystems. Although the importance of blue carbon within these ecosystems has been addressed in some countries of Southeast Asia, the regional and national inventories with the application of nature-based solutions are lacking. In this study, we aim to estimate national coastal blue carbon stocks in the seagrass ecosystems in the countries of Southeast Asia including the Andaman and Nicobar Islands of India. This study further assesses the potential of conservation and restoration practices and highlights the seagrass meadows as nature-based solution for climate change mitigation. The average value of the total carbon storage within seagrass meadows of this region is 121.95 ± 76.11 Mg ha-1 (average ± SD) and the total Corg stock of the seagrass meadows of this region was 429.11 ± 111.88 Tg, with the highest Corg stock in the Philippines (78%). The seagrass meadows of this region have the capacity to accumulate 5.85-6.80 Tg C year-1, which accounts for $214.6-249.4 million USD. Under the current rate of decline of 2.82%, the seagrass meadows are emitting 1.65-2.08 Tg of CO2 year-1 and the economic value of these losses accounts for $21.42-24.96 million USD. The potential of the seagrass meadows to the offset current CO2 emissions varies across the region, with the highest contribution to offset is in the seagrass meadows of the Philippines (11.71%). Current national policies and commitments of nationally determined contributions do not include blue carbon ecosystems as climate mitigation measures, even though these ecosystems can contribute up to 7.03% of the countries' reduction goal of CO2 emissions by 2030. The results of this study highlight and promote the potential of the southeast Asian seagrass meadows to national and international agencies as a practical scheme for nature-based solutions for climate change mitigation.

Two decades of seagrass area change: Organic carbon sources and stock.

Although seagrass ecosystems provide various ecosystem services, the implications in correspondence with temporal changes of the meadows is lacking. In this study, we analyzed two-decade changes of the seagrass area with the organic carbon storage and the sources at Libong island in Thailand. The seagrass area covered 841 ha in 2019, after two decades of decline (3.2 and 0.6% yr-1 between 2004 and 2009 and 2009-2019, respectively). Although δ13C was not significant between depth layers (p > 0.05), the general trend suggested that the terrestrial source of carbon is dominating bottom depth layer (31.7-37.2%), mixture of terrestrial (19.7-30.3%), seagrass (22.9-29.6%), mangrove (16.8-43.0%) and CPOM (11.2-25.4%) in the middle, and mangroves and seagrasses are dominating surface layer (28.3-66.2 and 29.3-36.5%, respectively). These trends approximately correspond to the areal changes of the meadows, as well as changes of urban area and water quality, providing detailed information on the meadow changes and possible causes.

Coastal and estuarine blue carbon stocks in the greater Southeast Asia region: Seagrasses and mangroves per nation and sum of total.

Climate Change solutions include CO2 extraction from atmosphere and water with burial by living habitats in sediment/soil. Nowhere on the planet are blue carbon plants which carry out massive carbon extraction and permanent burial more intensely concentrated than in SE Asia. For the first time we make a national and total inventory of data to date for "blue carbon" buried from mangroves and seagrass and delineate the constraints. For an area across Southeast Asia of approximately 12,000,000 km2, supporting mangrove forests (5,116,032 ha) and seagrass meadows (6,744,529 ha), we analyzed the region's current blue carbon stocks. This estimate was achieved by integrating the sum of estuarine in situ carbon stock measurements with the extent of mangroves and seagrass across each nation, then summed for the region. We found that mangroves ecosystems regionally supported the greater amount of organic carbon (3095.19Tg Corg in 1st meter) over that of seagrass (1683.97 Tg Corg in 1st meter), with corresponding stock densities ranging from 15 to 2205 Mg ha-1 and 31.3 to 2450 Mg ha-1 respectively, a likely underestimate for entire carbon including sediment depths. The largest carbon stocks are found within Indonesia, followed by the Philippines, Papua New Guinea, Myanmar, Malaysia, Thailand, Tropical China, Viet-Nam, and Cambodia. Compared to the blue carbon hotspot of tropical/subtropical Gulf of Mexico's total carbon stock (480.48 Tg Corg), Southeast Asia's greater mangrove-seagrass stock density appears a more intense Blue Carbon hotspot (4778.66 Tg Corg). All regional Southeast Asian nation states should assist in superior preservation and habitat restoration plus similar measures in the USA & Mexico for the Gulf of Mexico, as apparently these form two of the largest tropical carbon sinks within coastal waters. We hypothesize it is SE Asia's regionally unique oceanic-geologic conditions, placed squarely within the tropics, which are largely responsible for this blue carbon hotspot, that is, consistently high ambient light levels and year-long warm temperatures, together with consistently strong inflow of dissolved carbon dioxide and upwelling of nutrients across the shallow geological plates.

Longevity and sustainability of tropical and subtropical restored seagrass beds among Atlantic, Pacific, and Indian Oceans.

Seagrass longevity up to 47 years in well-restored, well-sited seagrass restorations are demonstrated from 253 trials at 83 regional sites in tropical and subtropical portions of three oceans (Atlantic, Pacific, Indian Oceans). These trials include over 3.04 million planted units into 306.3 ha. Approximately 12% of the total global tropical restored seagrass by Van Katwijk, Thorhaug et al. (2016) calculations from 1786 trials are included. Almost all projects herein reviewed persisted since date of planting except several cases with harsh anthropogenic impact or forceful natural events in first post-planting months. The oldest tropical/subtropical restoration continually observed is 47 yrs, many are 35 yrs. An array of observed and/or measured restored services accompanied these. This review may provide informational background for government resource managers, legislators, scientists, and citizens concerning tropical/subtropical seagrass longevity. This data from these trials may substantiate future seagrass restoration investments. Public outreach, national & regional government training,and outreach occurred, needing continuation.

Coralline macroalgae contribution to ecological services of carbon storage in a disturbed seagrass meadow.

Coralline macroalgae are globally distributed rhodopyhtes that remove carbon from their immediate environment and transform it into carbonate sediments through the senescence of their calcified tissues. In this study, the calcium carbonate (CaCO3) stocks in the tissue of Jania adhaerens and sediments in Tanjung Adang Shoal, Johor were quantified for a 13-month study period. The detailed maps of the geographical distribution based on the spatial and temporal variations of biomass and CaCO3 were also assessed. The highest amount of biomass, CaCO3 and organic carbon (OC) stocks in the tissues showed the highest in May 2018 and May 2019. The biomass values ranged from 65 to 143 g DW m-2, which contained 53-147 g CaCO3 m-2 and 3-11 g OC m-2. These findings provided insights into the biogeochemical cycling of these inputs, which can be used to estimate the overall carbon budget of the macrophyte meadow.

Comparison of the effects of calcified green macroalga (Halimeda macroloba Decaisne) and commercial CaCO3 on the properties of composite starch foam trays.

The calcified green macroalga, Halimeda macroloba, is a source of bio-based calcium carbonate which can be used as a filler in starch foam tray. In the first part of this study, the composition and structure of calcium carbonate of this species were investigated using Fourier transform infrared spectrometry (FTIR), X-ray diffraction (XRD), Energy dispersive X-ray spectroscopy (EDX) and Scanning election microscopy (SEM). The morphology of the macroalgal powder particles was rod-like and organic materials (e.g. polysaccharide) and calcium carbonate (aragonite form) were present. The second part of the study investigated the effects of calcium carbonate from H. macroloba on the properties of starch foam tray and compared them with the properties of starch foam tray filled with commercial CaCO3. Interestingly, the composites starch foam trays with macroalgal powder had better impact strength than starch/commercial CaCO3 composite foam trays. Moreover, the macroalgal powder affected the thermal properties of the starch foam tray equally as well as commercial CaCO3. However, the macroalgal powder caused more significant changes in the color parameters and the whiteness values of starch foam tray than commercial CaCO3.

Genetic species identification and population structure of Halophila (Hydrocharitaceae) from the Western Pacific to the Eastern Indian Ocean.

BACKGROUND: The Indo-Pacific region has the largest number of seagrass species worldwide and this region is considered as the origin of the Hydrocharitaceae. Halophila ovalis and its closely-related species belonging to the Hydrocharitaceae are well-known as a complex taxonomic challenge mainly due to their high morphological plasticity. The relationship of genetic differentiation and geographic barriers of H. ovalis radiation was not much studied in this region. Are there misidentifications between H. ovalis and its closely related species? Does any taxonomic uncertainty among different populations of H. ovalis persist? Is there any genetic differentiation among populations in the Western Pacific and the Eastern Indian Ocean, which are separated by the Thai-Malay peninsula? Genetic markers can be used to characterize and identify individuals or species and will be used to answer these questions. RESULTS: Phylogenetic analyses of the nuclear ribosomal internal transcribed spacer region based on materials collected from 17 populations in the Western Pacific and the Eastern Indian Ocean showed that some specimens identified as H. ovalis belonged to the H. major clade, also supported by morphological data. Evolutionary divergence between the two clades is between 0.033 and 0.038, much higher than the evolutionary divergence among H. ovalis populations. Eight haplotypes were found; none of the haplotypes from the Western Pacific is found in India and vice versa. Analysis of genetic diversity based on microsatellite analysis revealed that the genetic diversity in the Western Pacific is higher than in the Eastern Indian Ocean. The unrooted neighbor-joining tree among 14 populations from the Western Pacific and the Eastern Indian Ocean showed six groups. The Mantel test results revealed a significant correlation between genetic and geographic distances among populations. Results from band-based and allele frequency-based approaches from Amplified Fragment Length Polymorphism showed that all samples collected from both sides of the Thai-Malay peninsula were clustered into two clades: Gulf of Thailand and Andaman Sea. CONCLUSIONS: Our study documented the new records of H. major for Malaysia and Myanmar. The study also revealed that the Thai-Malay peninsula is a geographic barrier between H. ovalis populations in the Western Pacific and the Eastern Indian Ocean.

Development of chloroplast simple sequence repeats (cpSSRs) for the intraspecific study of Gracilaria tenuistipitata (Gracilariales, Rhodophyta) from different populations.

BACKGROUND: Gracilaria tenuistipitata is an agarophyte with substantial economic potential because of its high growth rate and tolerance to a wide range of environment factors. This red seaweed is intensively cultured in China for the production of agar and fodder for abalone. Microsatellite markers were developed from the chloroplast genome of G. tenuistipitata var. liui to differentiate G. tenuistipitata obtained from six different localities: four from Peninsular Malaysia, one from Thailand and one from Vietnam. Eighty G. tenuistipitata specimens were analyzed using eight simple sequence repeat (SSR) primer-pairs that we developed for polymerase chain reaction (PCR) amplification. FINDINGS: Five mononucleotide primer-pairs and one trinucleotide primer-pair exhibited monomorphic alleles, whereas the other two primer-pairs separated the G. tenuistipitata specimens into two main clades. G. tenuistipitata from Thailand and Vietnam were grouped into one clade, and the populations from Batu Laut, Middle Banks and Kuah (Malaysia) were grouped into another clade. The combined dataset of these two primer-pairs separated G. tenuistipitata obtained from Kelantan, Malaysia from that obtained from other localities. CONCLUSIONS: Based on the variations in repeated nucleotides of microsatellite markers, our results suggested that the populations of G. tenuistipitata were distributed into two main geographical regions: (i) populations in the west coast of Peninsular Malaysia and (ii) populations facing the South China Sea. The correct identification of G. tenuistipitata strains with traits of high economic potential will be advantageous for the mass cultivation of seaweeds.

A TAXONOMIC STUDY OF THE GENUS PADINA (DICTYOTALES, PHAEOPHYCEAE) INCLUDING THE DESCRIPTIONS OF FOUR NEW SPECIES FROM JAPAN, HAWAII, AND THE ANDAMAN SEA(1).

A taxonomic study of the genus Padina from Japan, Southeast Asia, and Hawaii based on morphology and gene sequence data (rbcL and cox3) resulted in the recognition of four new species, that is, Padina macrophylla and Padina ishigakiensis from Ryukyu Islands, Japan; Padina maroensis from Hawaii; and Padina usoehtunii from Myanmar and Thailand. All species are bistratose and morphologically different from one another as well as from any known taxa by a combination of characters relating to degree of calcification; the structure, position, and arrangement of hairlines (HLs) and reproductive sori; and the presence or absence of rhizoid-like groups of hairs and an indusium. Molecular phylogenetic analyses demonstrated a close relationship between P. ishigakiensis, P. macrophylla, P. maroensis, and Padina australis Hauck. The position of P. usoehtunii, however, was not fully resolved, being either sister to a clade comprising the other three new species and P. australis in the rbcL tree or more closely related to a clade comprising several other recently described species in the cox3 tree. The finding of the four new species demonstrates high species diversity particularly in southern Japan. The following characters were first recognized here to be useful for species delimitation: the presence or absence of small rhizoid-like groups of hairs on the thallus surface, structure and arrangement of HLs on both surfaces either alternate or irregular, and arrangement of the alternating HLs between both surfaces in equal or unequal distance. The evolutionary trajectory of these and six other morphological characters used in species delineation was traced on the phylogenetic tree.