Unearthing the sand microbiome of sea turtle nests with disparate survivorship at a mass-nesting beach in Costa Rica

2020 ◽  
Vol 85 ◽  
pp. 71-83
Author(s):  
VS Bézy ◽  
KM Hill-Spanik ◽  
CJ Plante
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Costa Rica ◽  
Hatching Success ◽  
Microbial Community Composition ◽  
Sea Turtle ◽  
Microbial Pathogens ◽  
Olive Ridley ◽  
Microbial Composition ◽  
Nesting Sites

For endangered sea turtle populations, microbial pathogens of developing embryos are of concern at nesting sites around the globe. For olive ridley turtles, hatching success is markedly lower at mass-nesting sites than at solitary nesting beaches, a case presumably resulting from the abundance of decomposing eggs generated by nesting turtles destroying adjacent eggs. This organic input drives microbial activity, affecting the nest environment (i.e. pO2 and temperature), and reducing embryo survivorship and hatching success. However, the composition of microbial communities in nest sand has not been studied in detail and the presence of potential pathogens can, therefore, not be discounted. As a part of a larger study that investigated microbial abundance in nests, we employed high-throughput DNA sequencing to compare fungal and bacterial composition in nest sand from areas of disparate embryo survivorship. While we found no differences in alpha-diversity (mean operational taxonomic unit diversity within each site) among nesting areas, the microbial community composition of each area was distinct, and differences in community structure corresponded with variable hatching success. Some sequences of potential sea turtle egg pathogens were obtained (e.g. Fusarium solani species complex), but were in low relative abundance, and their presence was not associated with low hatching success. Our results from the arribada beach at Ostional, Costa Rica, provide further evidence that the physical characteristics of the nest (including those that determine microbial composition and activity) are likely more relevant to hatching success than the presence of potential pathogens or microbial community structure alone.

scholarly journals Olive Ridley Sea Turtle Hatching Success as a Function of the Microbial Abundance in Nest Sand at Ostional, Costa Rica

PLoS ONE ◽  
2015 ◽  
Vol 10 (2) ◽  
pp. e0118579 ◽  
Author(s):  
Vanessa S. Bézy ◽  
Roldán A. Valverde ◽  
Craig J. Plante
Keyword(s):  
Costa Rica ◽  
Hatching Success ◽  
Sea Turtle ◽  
Microbial Abundance ◽  
Olive Ridley

scholarly journals Olive Ridley Sea Turtle Hatching Success as a Function of Microbial Abundance and the Microenvironment ofIn SituNest Sand at Ostional, Costa Rica

2014 ◽  
Vol 2014 ◽  
pp. 1-10 ◽  
Author(s):  
Vanessa S. Bézy ◽  
Roldán A. Valverde ◽  
Craig J. Plante
Keyword(s):  
Organic Matter ◽  
Costa Rica ◽  
Hatching Success ◽  
Quantitative Polymerase Chain Reaction ◽  
Organic Matter Content ◽  
Sea Turtle ◽  
High Density ◽  
Microbial Abundance ◽  
Olive Ridley ◽  
Nesting Beaches

Sea turtle hatching success at mass nesting beaches is typically lower than at solitary nesting beaches, presumably due in part to high rates of microbial metabolism resulting from the large input of organic matter from turtle eggs. Therefore, we tested the hypothesis that hatching success varies across areas of the beach in conjunction with differences in the physical nest environment and microbial abundance of in situ olive ridley sea turtle nests at Ostional, Costa Rica. We marked natural nests in high-density, low-density, and tidal-wash nesting areas of the beach and monitored clutch pO2and temperature throughout the incubation period. We quantified hatching success and collected samples of nest sand during nest excavations. We quantified microbial abundance (bacteria and fungi) with a quantitative polymerase chain reaction (qPCR) analysis. Hatching success was lower in nests with lower pO2, higher temperatures, higher organic matter content, and higher microbial abundance. Our results suggest that the lower oxygen within the nest environment is likely a result of the high microbial abundance and rates of decomposition in the nest sand and that these factors, along with increased temperature of clutches in the high-density nesting area, are collectively responsible for the low hatching success at Ostional.

scholarly journals Disentangling Responses of the Subsurface Microbiome to Wetland Status and Implications for Indicating Ecosystem Functions

2021 ◽  
Vol 9 (2) ◽  
pp. 211
Author(s):  
Jie Gao ◽  
Miao Liu ◽  
Sixue Shi ◽  
Ying Liu ◽  
Yu Duan ◽  
...  
Keyword(s):  
Microbial Community ◽  
High Throughput Sequencing ◽  
Carbon Fixation ◽  
Microbial Community Composition ◽  
Ecosystem Functions ◽  
Microbial Composition ◽  
Wetland Ecosystems ◽  
Soil Microbial ◽  
Geochemical Properties ◽  
Microbial Groups

In this study, we analyzed microbial community composition and the functional capacities of degraded sites and restored/natural sites in two typical wetlands of Northeast China—the Phragmites marsh and the Carex marsh, respectively. The degradation of these wetlands, caused by grazing or land drainage for irrigation, alters microbial community components and functional structures, in addition to changing the aboveground vegetation and soil geochemical properties. Bacterial and fungal diversity at the degraded sites were significantly lower than those at restored/natural sites, indicating that soil microbial groups were sensitive to disturbances in wetland ecosystems. Further, a combined analysis using high-throughput sequencing and GeoChip arrays showed that the abundance of carbon fixation and degradation, and ~95% genes involved in nitrogen cycling were increased in abundance at grazed Phragmites sites, likely due to the stimulating impact of urine and dung deposition. In contrast, the abundance of genes involved in methane cycling was significantly increased in restored wetlands. Particularly, we found that microbial composition and activity gradually shifts according to the hierarchical marsh sites. Altogether, this study demonstrated that microbial communities as a whole could respond to wetland changes and revealed the functional potential of microbes in regulating biogeochemical cycles.

scholarly journals Chelonicola and Poulinea, two new gomphonemoid diatom genera (Bacillariophyta) living on marine turtles from Costa Rica

Phytotaxa ◽  
2015 ◽  
Vol 233 (3) ◽  
pp. 236 ◽  
Author(s):  
Roksana Majewska ◽  
J. P. Kociolek ◽  
Evan W. Thomas ◽  
Mario De Stefano ◽  
Mario Santoro ◽  
...  
Keyword(s):  
Costa Rica ◽  
Marine Mammals ◽  
Sea Turtles ◽  
Sea Turtle ◽  
New Genera ◽  
Olive Ridley ◽  
Lepidochelys Olivacea ◽  
Marine Turtles ◽  
The Family ◽  
Long Time

Marine mammals such as whales and dolphins have been known for a long time to host a very specific epizoic community on their skin. Less known however is the presence of a similar community on the carapaces of sea turtles. The present study is the first describing new taxa inhabiting sea turtle carapaces. Samples, collected from nesting olive ridley sea turtles (Lepidochelys olivacea) on Ostional Beach (Costa Rica), were studied using light and scanning electron microscopy. Two unknown small-celled gomphonemoid taxa were analysed in more detail and are described as two new genera, closely related to other gomphonemoid genera with septate girdle bands, such as Tripterion, Cuneolus and Gomphoseptatum. Chelonicola Majewska, De Stefano & Van de Vijver gen. nov. has a flat valve face, uniseriate striae composed of more than three areolae, simple external raphe endings, internally a siliceous flap over the proximal raphe endings and lives on mucilaginous stalks. Poulinea Majewska, De Stefano & Van de Vijver gen. nov. has at least one concave valve, uniseriate striae composed of only two elongated areolae, external distal raphe endings covered by thickened siliceous flaps and lives attached to the substrate by a mucilaginous pad. Chelonicola costaricensis Majewska, De Stefano & Van de Vijver sp. nov. and Poulinea lepidochelicola Majewska, De Stefano & Van de Vijver sp. nov. can be separated based on stria structure, girdle structure composed of more than 10 copulae, raphe structure and general valve outline. A cladistics analysis of putative members of the Rhoicospheniaceae indicates that the family is polyphyletic. Chelonicola and Poulinea are sister taxa, and form a monophyletic group with Cuneolus and Tripterion, but are not closely related to Rhoicosphenia, or other genera previously assigned to this family. Features used to help diagnose the family such as symmetry and presence of septa and pseudosepta are homoplastic across the raphid diatom tree of life.

scholarly journals Compared the Microbiota Profiles between Samples from Bronchoalveolar Lavage and Endotracheal Aspirates in Severe Pneumonia: A Real-World Experience

2022 ◽  
Vol 11 (2) ◽  
pp. 327
Author(s):  
Yeong-Nan Cheng ◽  
Wei-Chih Huang ◽  
Chen-Yu Wang ◽  
Pin-Kuei Fu
Keyword(s):  
Microbial Community ◽  
Bronchoalveolar Lavage ◽  
Microbial Community Composition ◽  
Severe Pneumonia ◽  
Metagenomic Sequencing ◽  
Microbial Composition ◽  
Icu Patients ◽  
Mechanically Ventilated ◽  
The Difference ◽  
New Onset

Lower respiratory tract sampling from endotracheal aspirate (EA) and bronchoalveolar lavage (BAL) are both common methods to identify pathogens in severe pneumonia. However, the difference between these two methods in microbiota profiles remains unclear. We compared the microbiota profiles of pairwise EA and BAL samples in ICU patients with respiratory failure due to severe pneumonia. We prospectively enrolled 50 ICU patients with new onset of pneumonia requiring mechanical ventilation. EA and BAL were performed on the first ICU day, and samples were analyzed for microbial community composition via 16S rRNA metagenomic sequencing. Pathogens were identified in culture medium from BAL samples in 21 (42%) out of 50 patients. No difference was observed in the antibiotic prescription pattern, ICU mortality, or hospital mortality between BAL-positive and BAL-negative patients. The microbiota profiles in the EA and BAL samples are similar with respect to diversity, microbial composition, and microbial community correlations. The antibiotic treatment regimen was rarely changed based on the BAL findings. The samples from BAL did not provide more information than EA in the microbiota profiles. We suggest that EA is more useful than BAL for microbiome identification in mechanically ventilated patients.

scholarly journals Sea turtles support sustainable livelihoods at Ostional, Costa Rica

Oryx ◽  
2018 ◽  
Vol 53 (1) ◽  
pp. 81-91 ◽  
Author(s):  
Mallika Sardeshpande ◽  
Douglas MacMillan
Keyword(s):  
Costa Rica ◽  
Local Community ◽  
Sustainable Livelihoods ◽  
Household Survey ◽  
Sea Turtle ◽  
Environmental Conservation ◽  
Current Status ◽  
Structured Interviews ◽  
Olive Ridley ◽  
Nesting Site

AbstractOstional in Costa Rica is the second largest nesting site of the olive ridley sea turtle Lepidochelys olivacea, which is categorized as Vulnerable on the IUCN Red List. In Ostional the local community helps maintain the nesting site and collects olive ridley eggs for consumption and trade within Costa Rica. Since its inception in 1987 the egg harvesting project has integrated sea turtle conservation with community development. We assessed the current status of this project in terms of community awareness, dependency, involvement and perceptions, using a household survey and semi-structured interviews with key informants. We also compared some of our findings with those of previous studies at the site, finding that the project has fewer dependents, primary livelihood activities have shifted towards tourism and hospitality, and respondents are more aware about environmental conservation and stewardship. We map outcomes of the project with the Sustainable Livelihoods Framework, and suggest that further capacity building for research and tourism could contribute towards sustaining the turtle population, local livelihoods, and the community-based conservation institution.

scholarly journals Antibiotic resistome and microbial community structure during anaerobic co-digestion of food waste, paper and cardboard

2020 ◽  
Vol 96 (2) ◽  
Author(s):  
Kärt Kanger ◽  
Nigel G H Guilford ◽  
HyunWoo Lee ◽  
Camilla L Nesbø ◽  
Jaak Truu ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Solid State ◽  
Food Waste ◽  
Microbial Community Structure ◽  
Microbial Community Composition ◽  
Microbial Community Analysis ◽  
Waste Paper ◽  
Rrna Gene ◽  
Significant Shift

ABSTRACT Solid organic waste is a significant source of antibiotic resistance genes (ARGs) and effective treatment strategies are urgently required to limit the spread of antimicrobial resistance. Here, we studied ARG diversity and abundance as well as the relationship between antibiotic resistome and microbial community structure within a lab-scale solid-state anaerobic digester treating a mixture of food waste, paper and cardboard. A total of 10 samples from digester feed and digestion products were collected for microbial community analysis including small subunit rRNA gene sequencing, total community metagenome sequencing and high-throughput quantitative PCR. We observed a significant shift in microbial community composition and a reduction in ARG diversity and abundance after 6 weeks of digestion. ARGs were identified in all samples with multidrug resistance being the most abundant ARG type. Thirty-two per cent of ARGs detected in digester feed were located on plasmids indicating potential for horizontal gene transfer. Using metagenomic assembly and binning, we detected potential bacterial hosts of ARGs in digester feed, which included Erwinia, Bifidobacteriaceae, Lactococcus lactis and Lactobacillus. Our results indicate that the process of sequential solid-state anaerobic digestion of food waste, paper and cardboard tested herein provides a significant reduction in the relative abundance of ARGs per 16S rRNA gene.

scholarly journals Coupled changes in soil organic carbon fractions and microbial community composition in urban and suburban forests

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Xueying Zhang ◽  
Xiaomei Chen ◽  
Muying Liu ◽  
Zhanying Xu ◽  
Hui Wei
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Organic Carbon ◽  
Soil Organic Carbon ◽  
Community Composition ◽  
Microbial Community Structure ◽  
Soil Microorganisms ◽  
Microbial Community Composition ◽  
Soil C ◽  
Suburban Forests

Abstract Climate change and rapid urbanization have greatly impacted urban forest ecosystems and the carbon (C) cycle. To assess the effects of urbanization on forest soil C and soil microorganisms, six natural forests in a highly-urbanized region were selected as the research objects. Soil samples were collected to investigate the content and fractions of the soil organic carbon (SOC), as well as the soil microbial community composition. The results showed that the SOC content and fractions were substantially lower in the urban forests than in the suburban forests. Meanwhile, the total amount of phospholipid fatty acids (PLFAs) at suburban sites was twice more than that at urban sites, with shifts in microbial community structure. The potential differences in C inputs and nutrient limitation in urban forests may aggravate the low quantity and quality of SOC and consequently impact microbial community abundance and structure. Variation in microbial community structure was found to explain the loss of soil C pools by affecting the C inputs and promoting the decomposition of SOC. Therefore, the coupled changes in SOC and soil microorganisms induced by urbanization may adversely affect soil C sequestration in subtropical forests.

scholarly journals PSI-10 Establishing a foundation to harvest the potential of the microbiome in poultry production

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 293-294
Author(s):  
Camila S Marcolla ◽  
Benjamin Willing
Keyword(s):  
Microbial Community ◽  
Gut Microbiota ◽  
Community Composition ◽  
Relative Abundance ◽  
Microbial Community Composition ◽  
Alpha Diversity ◽  
Poultry Production ◽  
Microbiota Composition ◽  
Microbial Composition ◽  
The Impact

Abstract This study aimed to characterize poultry microbiota composition in commercial farms using 16S rRNA sequencing. Animals raised in sanitized environments have lower survival rates when facing pathogenic challenges compared to animals naturally exposed to commensal organisms. We hypothesized that intensive rearing practices inadvertently impair chicken exposure to microbes and the establishment of a balanced gut microbiota. We compared gut microbiota composition of broilers (n = 78) and layers (n = 20) from different systems, including commercial intensive farms with and without in-feed antibiotics, organic free-range farms, backyard-raised chickens and chickens in an experimental farm. Microbial community composition of conventionally raised broilers was significantly different from antibiotic-free broilers (P = 0.012), from broilers raised outdoors (P = 0.048) and in an experimental farm (P = 0.006) (Fig1). Significant community composition differences were observed between antibiotic-fed and antibiotic-free chickens (Fig2). Antibiotic-free chickens presented higher alpha-diversity, higher relative abundance of Deferribacteres, Fusobacteria, Bacteroidetes and Actinobacteria, and lower relative abundance of Firmicutes, Clostridiales and Enterobacteriales than antibiotic-fed chickens (P < 0.001) (Fig3). Microbial community composition significantly changed as birds aged. In experimental farm, microbial community composition was significant different for 7, 21 and 35 day old broilers (P < 0.001), and alpha diversity increased from 7 to 21d (P < 0.024), but not from 21 to 35d; whereas, in organic systems, increases in alpha-diversity were observed from 7d to 21d, and from 21d to 35d (P < 0.05). Broilers and layers raised together showed no differences in microbiota composition and alpha diversity (P > 0.8). It is concluded that production practices consistently impact microbial composition, and that antibiotics significantly reduces microbial diversity. We are now exploring the impact of differential colonization in a controlled setting, to determine the impact of the microbes associated with extensively raised chickens. This study will support future research and the development of methods to isolate and introduce beneficial microbes to commercial systems.

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