Too hot to handle? An urgent need to understand climate change impacts on the biogeochemistry of tropical coastal waters.

Tropical regions contain ecologically and socio-economically important habitats, and are home to about 3.8 billion people, many of which directly depend on tropical coastal waters for their well-being. At the basis of these ecosystems are biogeochemical processes. Climate change is expected to have a greater impact in the tropics compared to temperate regions because of the relatively stable environmental conditions found there. However, it was surprising to find only 660 research articles published focusing on the impact of climate change on the biogeochemistry of coastal tropical waters compared to 4823 for temperate waters. In this perspective, we highlight important topics in need of further research. Specifically, we suggest that in tropical regions compared to temperate counterparts climate change stressors will be experienced differently, that organisms have a lower acclimation capacity, and that long-term baseline biogeochemical datasets useful for quantifying future changes are lacking. The low number of research papers on the impacts of climate change in coastal tropical regions is likely due to a mix of reasons including limited resources for research and limited number of long time series in many developing tropical countries. Finally, we propose some action points that we hope will stimulate more studies in tropical coastal waters.

Meeting report: The first soil viral workshop 2022.

Soil viral ecology is a growing research field; however, the state of knowledge still lags behind that of aquatic systems. Therefore, to facilitate progress, the first Soil Viral Workshop was held to encourage international scientific discussion and collaboration, suggest guidelines for future research, and establish soil viral research as a concrete research area. The workshop took place at Søminestationen, Denmark, between 15 and 17th of June 2022. The meeting was primarily held in person, but the sessions were also streamed online. The workshop was attended by 23 researchers from ten different countries and from a wide range of subfields and career stages. Eleven talks were presented, followed by discussions revolving around three major topics: viral genomics, virus-host interactions, and viruses in the soil food web. The main take-home messages and suggestions from the discussions are summarized in this report.

Starting gastrointestinal endoscopy in a lower middle-income country in Africa: Training, creating an endoscopy facility and developing telemedicine.

Background and study aims The prevalence of digestive diseases seems to be high in African countries. Nonetheless, the human and material resources are scarce. The aim of the Portuguese volunteering project described in this report was to develop the specialty of digestive endoscopy in Sao Tome and Principe, a lower-middle-income country in Africa. Methods Beginning by assessing the local needs and available resources and managing immediate issues related to this field, we aimed to provide the tools necessary to improve gastroenterological and endoscopic care in the country. The first step included training of the local teams, through the development and accomplishment of an adapted curriculum for a 3-year medical gastroenterological fellowship and a short-term nursing fellowship, both in Portugal, and the organization of regular gastroenterological and endoscopic theoretical and practical sessions in Sao Tome and Principe. Second, the endoscopy facilities of the unit were significantly optimized. Third, a web platform was designed to provide telemedicine incorporating real-time endoscopic imaging available remotely. Results Through these sequential steps achieved in collaboration with Portuguese and local teams, this 5-year project provided the basis for gastroenterology care in this country. Conclusions At the present time, Sao Tome and Principe has an autonomous, efficient and skilled team and unit to provide care for patients with gastrointestinal diseases who need endoscopic procedures.

Small-scale distribution of microbes and biogeochemistry in the Great Barrier Reef.

Microbial communities distribute heterogeneously at small-scales (mm-cm) due to physical, chemical and biological processes. To understand microbial processes and functions it is necessary to appreciate microbes and matter at small scales, however, few studies have determined microbial, viral, and biogeochemical distribution over space and time at these scales. In this study, the small-scale spatial and temporal distribution of microbes (bacteria and chlorophyll a), viruses, dissolved inorganic nutrients and dissolved organic carbon were determined at five locations (spatial) along the Great Barrier Reef (Australia), and over 4 consecutive days (temporal) at a coastal location. Our results show that: (1) the parameters show high small-scale heterogeneity; (2) none of the parameters measured explained the bacterial abundance distributions at these scales spatially or temporally; (3) chemical (ammonium, nitrate/nitrite, phosphate, dissolved organic carbon, and total dissolved nitrogen) and biological (chl a, and bacterial and viral abundances) measurements did not reveal significant relationships at the small scale; and (4) statistically significant differences were found between sites/days for all parameter measured but without a clear pattern.

Fungi and viruses as important players in microbial mats.

Microbial mats are compacted, surface-associated microbial ecosystems reminiscent of the first living communities on early Earth. While often considered predominantly prokaryotic, recent findings show that both fungi and viruses are ubiquitous in microbial mats, albeit their functional roles remain unknown. Fungal research has mostly focused on terrestrial and freshwater ecosystems where fungi are known as important recyclers of organic matter, whereas viruses are exceptionally abundant and important in aquatic ecosystems. Here, viruses have shown to affect organic matter cycling and the diversity of microbial communities by facilitating horizontal gene transfer and cell lysis. We hypothesise fungi and viruses to have similar roles in microbial mats. Based on the analysis of previous research in terrestrial and aquatic ecosystems, we outline novel hypotheses proposing strong impacts of fungi and viruses on element cycling, food web structure and function in microbial mats, and outline experimental approaches for studies needed to understand these interactions.

Endoprotector: Protective box for safe endoscopy use during COVID-19 outbreak.

Background and study aim Outbreak of COVID-19 began in Wuhan in December 2019 and has rapidly spread from China to the rest of the world. Although it is primarily transmitted by contact and droplets, aerosol-generating procedures also seem to carry the possibility of airborne viral transmission. As such, upper gastrointestinal endoscopy can be considered a risky procedure, with several position statements recommending the adoption of safe practices in endoscopic procedures. This article aims to describe an additional tool to protect healthcare personnel during endoscopy. Methods A covering box made of acrylic plastic, named Endoprotector, was designed to cover the patient's head, while taking into consideration movements performed by patients and healthcare staff during an endoscopic procedure. Results A cough simulation using fluorescent dye confirmed the potential benefit of the box during endoscopy, thus protecting healthcare staff from air droplets. The feasibility and practicality of the box was also tested with patients during endoscopy. Conclusion The reusable Endoprotector is easily and affordably manufactured and may reduce air droplets and airborne transmission of SARS-CoV-2 and other microorganisms during endoscopy.

Responses of physiological groups of tropical heterotrophic bacteria to temperature and dissolved organic matter additions: food matters more than warming.

Compared to higher latitudes, tropical heterotrophic bacteria may be less responsive to warming because of strong bottom-up control. In order to separate both drivers, we determined the growth responses of bacterial physiological groups to temperature after adding dissolved organic matter (DOM) from mangroves, seagrasses and glucose to natural seawater from the Great Barrier Reef. Low (LNA) and high (HNA) nucleic acid content, membrane-intact (Live) and membrane-damaged (Dead) plus actively respiring (CTC+) cells were monitored for 4 days. Specific growth rates of the whole community were significantly higher (1.9 day-1 ) in the mangrove treatment relative to the rest (0.2-0.4 day-1 ) at in situ temperature and their temperature dependence, estimated as activation energy, was also consistently higher. Strong bottom-up control was suggested in the other treatments. Cell size depended more on DOM than temperature. Mangrove DOM resulted in significantly higher contributions of Live, HNA and CTC+ cells to total abundance, while the seagrass leachate reduced Live cells below 50%. Warming significantly decreased Live and CTC+ cells contributions in most treatments. Our results suggest that only in the presence of highly labile compounds, such as mangroves DOM, can we anticipate increases in heterotrophic bacteria biomass in response to warming in tropical regions.

Dissolved Organic Carbon Source Influences Tropical Coastal Heterotrophic Bacterioplankton Response to Experimental Warming.

Global change impacts on marine biogeochemistry will be partly mediated by heterotrophic bacteria. Besides ocean warming, future environmental changes have been suggested to affect the quantity and quality of organic matter available for bacterial growth. However, it is yet to be determined in what way warming and changing substrate conditions will impact marine heterotrophic bacteria activity. Using short-term (4 days) experiments conducted at three temperatures (-3°C, in situ, +3°C) we assessed the temperature dependence of bacterial cycling of marine surface water used as a control and three different dissolved organic carbon (DOC) substrates (glucose, seagrass, and mangrove) in tropical coastal waters of the Great Barrier Reef, Australia. Our study shows that DOC source had the largest effect on the measured bacterial response, but this response was amplified by increasing temperature. We specifically demonstrate that (1) extracellular enzymatic activity and DOC consumption increased with warming, (2) this enhanced DOC consumption did not result in increased biomass production, since the increases in respiration were larger than for bacterial growth with warming, and (3) different DOC bioavailability affected the magnitude of the microbial community response to warming. We suggest that in coastal tropical waters, the magnitude of heterotrophic bacterial productivity and enzyme activity response to warming will depend partly on the DOC source bioavailability.

Microscale spatial distributions of microbes and viruses in intertidal photosynthetic microbial mats.

Intertidal photosynthetic microbial mats from the Wadden Sea island Schiermonnikoog were examined for microscale (millimetre) spatial distributions of viruses, prokaryotes and oxygenic photoautotrophs (filamentous cyanobacteria and benthic diatoms) at different times of the year. Abundances of viruses and prokaryotes were among the highest found in benthic systems (0.05-5.43 × 10(10) viruses g(-1) and 0.05-2.14 × 10(10) prokaryotes g(-1)). The spatial distribution of viruses, prokaryotes and oxygenic photoautotrophs were highly heterogeneous at mm scales. The vertical distributions of both prokaryotic and viral abundances were related to the depth of the oxygenic photoautotrophic layer, implying that the photosynthetic mat fuelled the microbial processes in the underlying layer. Our data suggest that viruses could make an important component in these productive environments potentially affecting the biodiversity and nutrient cycling within the mat.

Disruption of photoautotrophic intertidal mats by filamentous fungi.

Ring-like structures, 2.0-4.8 cm in diameter, observed in photosynthetic microbial mats on the Wadden Sea island Schiermonnikoog (the Netherlands) showed to be the result of the fungus Emericellopsis sp. degrading the photoautotrophic top layer of the mat. The mats were predominantly composed of cyanobacteria and diatoms, with large densities of bacteria and viruses both in the top photosynthetic layer and in the underlying sediment. The fungal attack cleared the photosynthetic layer; however, no significant effect of the fungal lysis on the bacterial and viral abundances could be detected. Fungal-mediated degradation of the major photoautotrophs could be reproduced by inoculation of non-infected mat with isolated Emericellopsis sp., and with an infected ring sector. Diatoms were the first re-colonizers followed closely by cyanobacteria that after about 5 days dominated the space. The study demonstrated that the fungus Emericellopsis sp. efficiently degraded a photoautotrophic microbial mat, with potential implications for mat community composition, spatial structure and productivity.

Counting viruses and bacteria in photosynthetic microbial mats.

Viral abundances in benthic environments are the highest found in aquatic systems. Photosynthetic microbial mats represent benthic environments with high microbial activity and possibly high viral densities, yet viral abundances have not been examined in such systems. Existing extraction procedures typically used in benthic viral ecology were applied to the complex matrix of microbial mats but were found to inefficiently extract viruses. Here, we present a method for extraction and quantification of viruses from photosynthetic microbial mats using epifluorescence microscopy (EFM) and flow cytometry (FCM). A combination of EDTA addition, probe sonication, and enzyme treatment applied to a glutaraldehyde-fixed sample resulted in a substantially higher viral (5- to 33-fold) extraction efficiency and reduced background noise compared to previously published methods. Using this method, it was found that in general, intertidal photosynthetic microbial mats harbor very high viral abundances (2.8 × 10(10) ± 0.3 × 10(10) g(-1)) compared with benthic habitats (10(7) to 10(9) g(-1)). This procedure also showed 4.5- and 4-fold-increased efficacies of extraction of viruses and bacteria, respectively, from intertidal sediments, allowing a single method to be used for the microbial mat and underlying sediment.

Preparation and characterization of DNA films using oleylamine modified Au surfaces.

Thin films composed of oleylamine (OLA) and double-stranded deoxyribonucleic acid (dsDNA from Salmon testes) have been successfully constructed on polycrystalline Au surfaces using the electrostatic adsorption and self-assembly (SA) technique. The formation of the Au/OLA/dsDNA films was followed step-by-step by Quartz Crystal Microbalance with energy dissipation (QCM-D), Atomic Force Microscopy (AFM), and electrochemical techniques such as Cyclic Voltammetry (CV) and Electrochemical Impedance Spectroscopy (EIS). The use of these techniques allowed the characterization and the follow up of the successful construction of the OLA/dsDNA composite film. The main advantages of the proposed methodology are the simplicity of the modification procedure, the stability of the dsDNA self-assembled film, and the potential employment of the dsDNA modified gold electrodes to study the interactions of DNA with target molecules.