Intertidal microphytobenthic primary production and net metabolism of a tropical estuary.

Tidal flats are inhabited by benthic microalgae (microphytobenthos, MPB) supporting important ecosystem functions and services. Studies on MPB have been conducted mainly in temperate systems, despite that the majority of tidal flats on Earth are found in the tropical zone (∼55%). To fill this gap of knowledge and evaluate the contribution of tidal flat MPB in one of the most productive estuaries worldwide, sediment cores were collected from 14 stations along the inner Gulf of Nicoya (Costa Rica) at different tidal heights or sea levels (SL) from October 2013 to April 2014. MPB abundance, using chlorophyll a (Chla) biomass as a proxy, and net primary production (PN) and dark respiration (RD), using O2 microsensors, were measured together with other sediment biogeochemical variables in muddy and sandy sediments. Landsat-8 satellite images were used to map the extension of tidal flats and the abundance of MPB using Normalized Difference Vegetation Index (NDVI) as a proxy. Chla ranged from 0.45 to 7.45 µg cm-2, with higher concentrations observed closer to the river mouth. There was no significant correlation between Chla and SL nor with any other sediment physicochemical variable. MPB abundance estimated by remote sensing displayed considerable spatial heterogeneity, both within and among tidal flats, and clear seasonal differences with higher abundance during the rainy season. PN ranged between 0.8 and 8.6 mmol O2 m-2 h-1, being positively correlated to SL and to the accumulated rain during 30 days prior to the sampling date and inversely to the mean irradiance at noon during the previous month. Daily net community metabolism estimated from PN and RD data and converted to carbon fixation rates indicates that the unvegetated tidal flats of the gulf contribute as much as the total input of allochthonous C from the Tempisque River. However, the results presented here have to be confirmed with direct measurements of C transfer, including the contribution of the adjacent mangrove system. Such studies are crucial to assess the local, regional and global importance of production and other ecosystem services by MPB in tropical areas.

Unraveling antibiotic resistomes associated with bacterial and viral communities in intertidal mudflat aquaculture area.

The extensive use of antibiotics in intertidal mudflat aquaculture area has substantially increased the dissemination risk of antibiotic resistance genes (ARGs). As hosts of ARGs, bacteria and virus exert vital effects on ARG dissemination. However, the insights for the interrelationships among ARGs, bacteria, and virus have not been thoroughly explored in intertidal mudflat. Therefore, this study attempts to unravel the occurrence, dissemination, evolution, and driving mechanisms of ARGs associated with bacterial and viral communities using metagenomic sequencing in a typical intertidal mudflat. Abundant and diverse ARGs (22 types and 437 subtypes) were identified and those of ARGs were higher in spring than in autumn. It is worthy noted that virus occupied a more essential position than bacteria for ARGs dissemination through network analysis. Meanwhile, nitrogen exerted indirect effect on ARG profiles by shaping viral and bacterial diversity. According to the results of neutral and null models, deterministic processes dominated the ARG community assembly by controlling sediment nitrogen and antibiotics. Homogeneous and variable selection dominated phylogenetic turnover of ARG community, contributing 46.15% and 45.90% of the total processes, respectively. This study can hence theoretically support for the ARG pollution control and management in intertidal mudflat aquaculture area.

Taeanamides A and B, Nonribosomal Lipo-Decapeptides Isolated from an Intertidal-Mudflat-Derived Streptomyces sp.

Two new lipo-decapeptides, namely taeanamides A and B (1 and 2), were discovered from the Gram-positive bacterium Streptomyces sp. AMD43, which was isolated from a mudflat sample from Anmyeondo, Korea. The exact molecular masses of 1 and 2 were revealed by high-resolution mass spectrometry, and the planar structures of 1 and 2 were elucidated using NMR spectroscopy. The absolute configurations of 1 and 2 were determined using a combined analysis of 1H-1H coupling constants and ROESY correlations, the advanced Marfey's method, and bioinformatics. The putative nonribosomal peptide synthetase pathway for the taeanamides was identified by analyzing the full genome sequence data of Streptomyces sp. AMD43. We also found that taeanamide A exhibited mild anti-tuberculosis bioactivity, whereas taeanamide B showed significant bioactivity against several cancer cell lines.

Microbial Communities and Diversities in Mudflat Sediments Analyzed Using a Modified Metatranscriptomic Method.

Intertidal mudflats are land-sea interaction areas and play important roles in global nutrient cycles. However, a comprehensive understanding of microbial communities in these mudflats remains elusive. In this study, mudflat sediment samples from the Dongtan wetland of Chongming Island, the largest alluvial island in the world, were collected. Using a modified metatranscriptomic method, the depth-wise distributions of potentially active microbial communities were investigated based on small subunit ribosomal RNA (SSU rRNA) sequences. Multiple environmental factors were also measured and analyzed in conjunction with the prokaryotic composition profiles. A prokaryotic diversity analysis based on the metatranscriptome datasets revealed two or threefold higher diversity indices (associated with potentially active microbes participating in biogeochemical processes in Dongtan) compared with the diversity indices based on 16S rRNA gene amplicons. Bacteria were numerically dominant relative to archaea, and the potentially active prokaryotic taxa were mostly assigned to the bacterial phyla Chloroflexi, Acidobacteria, and Bacteroidetes and the classes Delta- and Gamma-proteobacteria, along with the archaeal lineages phylum Bathyarchaeota and the order Thermoplasmatales. The total nitrogen and carbon content of the sediment samples were environmental factors that significantly affected the depth-wise distributions of both bacterial and archaeal communities. Furthermore, the activity of potentially active taxa (including the prevalent order Desulfobacterales and family Anaerolineaceae) appeared to be significantly underestimated by PCR-based methods, notably at the DNA level, and indicates that using normal PCR amplification of DNA limits the study of potential microbial activity. This is the first study of potentially active microbial communities in depth-wise sediments from Dongtan. The improved knowledge of microbial communities in Dongtan provides a foundation for exploring biogeochemical cycling and microbial functions.

Diel Rhythm Does Not Shape the Vertical Distribution of Bacterial and Archaeal 16S rRNA Transcript Diversity in Intertidal Sediments: a Mesocosm Study.

In intertidal sediments, circadian oscillations (i.e., tidal and diel rhythms) and/or depth may affect prokaryotic activity. However, it is difficult to distinguish the effect of each single force on active community changes in these natural and complex intertidal ecosystems. Therefore, we developed a tidal mesocosm to control the tidal rhythm and test whether diel fluctuation or sediment depth influence active prokaryotes in the top 10 cm of sediment. Day- and nighttime emersions were compared as they are expected to display contrasting conditions through microphytobenthic activity in five different sediment layers. A multiple factor analysis revealed that bacterial and archaeal 16S ribosomal RNA (rRNA) transcript diversity assessed by pyrosequencing was similar between day and night emersions. Potentially active benthic Bacteria were highly diverse and influenced by chlorophyll a and phosphate concentrations. While in oxic and suboxic sediments, Thaumarchaeota Marine Group I (MGI) was the most active archaeal phylum, suggesting the importance of the nitrogen cycle in muddy sediments, in anoxic sediments, the mysterious archaeal C3 group dominated the community. This work highlighted that active prokaryotes organize themselves vertically within sediments independently of diel fluctuations suggesting adaptation to physicochemical-specific conditions associated with sediment depth.

Two new species of benthopelagic Stephos (Copepoda, Calanoida, Stephidae) from Korea.

Two new species of benthopelagic copepods of the genus Stephos T. Scott, 1892, belonging to the family Stephidae G.O. Sars, 1902, are described based on specimens collected in the stagnant water flooding the burrows excavated by ocypodid crabs in two intertidal mud-flats, and from near-bottom shallow waters in Korea, respectively. They can be easily diagnosed based on the ornamentation of both the female genital double-somite and genital operculum; the morphology of the distal segment of the male right P5; the presence/absence of a tiny pointed process on the distomedial angle of second segment of female P5; and the condition (seta or spine) of the lateral armature element on the distal segment of female fifth legs, among other features. This is one of the few cases reported of calanoid copepods living as commensals of other invertebrates, and raises to six the number of members of the genus reported from Asia. This is also the first record of the family Stephidae in Korea.

Response of microbial communities to bioturbation by artificially introducing macrobenthos to mudflat sediments for in situ bioremediation in a typical semi-enclosed bay, southeast China.

Although microbes play important roles during the bioremediation process using macrobenthos in degraded environments, their response to macrobenthos bioturbation remains poorly understood. This study used 16S rRNA gene-Illumina Miseq sequencing to investigate the microbial communities and their response to bioturbation by artificially introducing macrobenthos to the mudflat of Sansha Bay, southeast China. A total of 56 phyla were identified, dominated by δ- and γ-Proteobacteria, with a total percentage of over 50%. Others, such as Acidobacteria, Chloroflexi, Bacteroidetes, Planctomycetes and Alphaproteobacteria occupied 4-7% respectively. Eighteen genera indicating the microbial communities response to bioturbation and seasonal change were identified. Bioturbated samples contained more ecologically important genera, and untreated samples contained more genera ubiquitous in marine environments. The physicochemical characteristics did not change significantly probably due to the short time of bioremediation and low survival rate of macrobenthos, confirming that microbial communities are more sensitive and can serve as sentinels for environmental changes.

Novel nonribosomal peptide synthetase (NRPS) genes sequenced from intertidal mudflat bacteria.

Nonribosomal peptide synthetases (NRPS) are actively sought out, due to pharmacologically important activities of their metabolites. In marine environment, the most prevalent nonribosomal peptide antibiotic producers are sponges inhabiting microorganisms. Conversely, strains from marine sediments and more especially from intertidal mudflats have not been extensively screened for the presence of new NRPS. In this study, for the first time, a collection of one hundred intertidal mudflat bacterial isolates (Marennes-Oléron Bay, France) was assessed for (1) the presence of NRPS genes by degenerated PCR targeting conserved adenylation domains and (2) for their production of antimicrobial molecules. (1) Bacteria with adenylation domains (14 strains) were identified by 16S rRNA gene sequence analysis and grouped into Firmicutes (one strain) and Proteobacteria (13 strains). In silico analysis of the NRPS amino acid sequences (n = 7) showed 41-58% ID with sequences found in the NCBI database. Three new putative adenylation domain signatures were found. (2) The culture supernatant of one of these strains, identified as a Bacillus, was shown to strongly inhibit the growth of Staphylococcus aureus, S. epidermidis, and Enterococcus faecalis. This study portends that the intertidal mudflat niche could be of interest for the discovery of new NRPS genes and antimicrobial producing strains.

Human trampling as short-term disturbance on intertidal mudflats: effects on macrofauna biodiversity and population dynamics of bivalves.

The effect of physical disturbance in the form of trampling on the benthic environment of an intertidal mudflat was investigated. Intense trampling was created as unintended side-effect by benthic ecologists during field experiments in spring and summer 2005, when a mid-shore area of 25 × 25 m was visited twice per month by on average five researchers for a period of 8 months. At the putatively-impacted location (I) (25 × 25 m) and two nearby control locations (Cs) (25 × 25 m each), three sites (4 × 4 m) were randomly selected and at each site, three plots (50 × 50 cm) were sampled after 18 and 40 days from the end of the disturbance. Multivariate and univariate asymmetrical analyses tested for changes in the macrofaunal assemblage, biomass of microphytobenthos and various sediment properties (grain-size, water content, NH4 and NO3 concentrations in the pore water) between the two control locations (Cs) and the putatively-impacted location (I). There were no detectable changes in the sediment properties and microphytobenthos biomass, but variability at small scale was observed. Microphytobenthos and NH4 were correlated at I to the number of footprints, as estimated by the percentage cover of physical depressions. This indicated that trampling could have an impact at small scales, but more investigation is needed. Trampling, instead, clearly modified the abundance and population dynamics of the clam Macoma balthica (L.) and the cockle Cerastoderma edule (L.). There was a negative impact on adults of both species, probably because footsteps directly killed or buried the animals, provoking asphyxia. Conversely, trampling indirectly enhanced recruitment rate of M. balthica, while small-sized C. edule did not react to the trampling. It was likely that small animals could recover more quickly because trampling occurred during the growing season and there was a continuous supply of larvae and juveniles. In addition, trampling might have weakened negative adult-juvenile interactions between adult cockles and juvenile M. balthica, thus facilitating the recruitment. Our findings indicated that human trampling is a relevant source of disturbance for the conservation and management of mudflats. During the growing season recovery can be fast, but in the long-term it might lead towards the dominance of M. balthica to the cost of C. edule, thereby affecting ecosystem functioning.