• Energy Research

Cette étude s'est concentrée sur les effets des amendements organiques et inorganiques et de la rétention de paille sur la biomasse microbienne (MB) et les groupes taxonomiques de bactéries dans les sols cultivés en canne à sucre dans une expérience de mésocosme de serre surveillée pour les émissions de gaz et les facteurs chimiques. L'expérience consistait en des combinaisons d'azote synthétique (N), de vinasse (V ; un déchet liquide provenant de la production d'éthanol) et de couvertures en paille de canne à sucre. Des augmentations des émissions de CO2-C et de N2O-N ont été identifiées peu de temps après l'ajout de N et de V aux sols, augmentant ainsi l'azote MB (MB-N) et diminuant le carbone MB (MB-C) dans les sols modifiés par N+ V et modifiant les facteurs chimiques du sol qui étaient corrélés avec le MB. Dans 57 ensembles de données métagénomiques du sol, les Actinobactéries (31,5 %), les Planctomycètes (12,3 %), les Deltaprotéobactéries (12,3 %), les Alphaprotéobactéries (12,0 %) et les Bétaprotéobactéries (11,1 %) étaient les groupes bactériens les plus dominants au cours de l'expérience. Les différences dans l'abondance relative des séquences métagénomiques ont été principalement révélées pour les Acidobactéries, les Actinobactéries, les Gammaproteobactéries et les Verrucomicrobies en ce qui concerne la fertilisation en N+V et la rétention de la paille. Les abondances différentielles dans les groupes bactériens ont été confirmées à l'aide d'amorces spécifiques au phylum ciblant le gène de l'ARNr 16S pour l'analyse PCR en temps réel dans tous les échantillons de sol, dont les résultats étaient conformes aux données de séquence, à l'exception des Gammaproteobacteria. Les Actinobactéries étaient plus sensibles à la rétention de paille chez les Rubrobacterales, les Bifidobacteriales et les Actinomycetales liée aux facteurs chimiques des sols modifiés en N+ V. Le sous-groupe 7 d'acidobactéries et Opitutae, une classe verrucomicrobienne, étaient liés aux facteurs chimiques des sols sans rétention de paille comme couverture de surface. Pris ensemble, les résultats ont montré que le MB-C et le MB-N répondaient aux changements des facteurs chimiques du sol et aux émissions de CO2-C et de N2O-N, en particulier pour les sols modifiés en N+ V. Les résultats ont également indiqué que plusieurs groupes taxonomiques de bactéries, tels que les Acidobactéries, les Actinobactéries et les Verrucomicrobia, et leurs sous-groupes ont agi comme des indicateurs d'alerte précoce des modifications de N+V et de la rétention de paille dans les sols cultivés en canne à sucre, ce qui peut modifier les facteurs chimiques du sol. Este estudio se centró en los efectos de las enmiendas orgánicas e inorgánicas y la retención de paja en la biomasa microbiana (MB) y los grupos taxonómicos de bacterias en suelos cultivados con caña de azúcar en un experimento de mesocosmos en invernadero monitoreado por emisiones de gases y factores químicos. El experimento consistió en combinaciones de nitrógeno sintético (N), vinaza (V; un residuo líquido de la producción de etanol) y mantas de paja de caña de azúcar. Los aumentos en las emisiones de CO2-C y N2O-N se identificaron poco después de la adición de N y V a los suelos, aumentando así el nitrógeno MB (MB-N) y disminuyendo el carbono MB (MB-C) en los suelos modificados con N+ V y alterando los factores químicos del suelo que se correlacionaron con el MB. En 57 conjuntos de datos metagenómicos del suelo, Actinobacteria (31.5%), Planctomycetes (12.3%), Deltaproteobacteria (12.3%), Alphaproteobacteria (12.0%) y Betaproteobacteria (11.1%) fueron los grupos bacterianos más dominantes durante el experimento. Las diferencias en la abundancia relativa de secuencias metagenómicas se revelaron principalmente para Acidobacteria, Actinobacteria, Gammaproteobacteria y Verrucomicrobia con respecto a la fertilización N+V y la retención de la paja. Las abundancias diferenciales en los grupos bacterianos se confirmaron utilizando cebadores específicos de filo dirigidos al gen de ARNr 16S para el análisis de PCR en tiempo real en todas las muestras de suelo, cuyos resultados estaban de acuerdo con los datos de secuencia, excepto para Gammaproteobacteria. Las actinobacterias fueron más sensibles a la retención de paja con Rubrobacterales, Bifidobacteriales y Actinomycetales relacionados con los factores químicos de los suelos modificados con N+ V. Acidobacterias subgrupo 7 y Opitutae, una clase verrucomicrobiana, se relacionaron con los factores químicos de los suelos sin retención de paja como manto superficial. En conjunto, los resultados mostraron que MB-C y MB-N respondieron a los cambios en los factores químicos del suelo y las emisiones de CO2-C y N2O-N, especialmente para los suelos modificados con N+ V. Los resultados también indicaron que varios grupos taxonómicos de bacterias, como Acidobacteria, Actinobacteria y Verrucomicrobia, y sus subgrupos actuaron como indicadores de alerta temprana de enmiendas N+V y retención de paja en suelos cultivados con caña de azúcar, lo que puede alterar los factores químicos del suelo. This study focused on the effects of organic and inorganic amendments and straw retention on the microbial biomass (MB) and taxonomic groups of bacteria in sugarcane-cultivated soils in a greenhouse mesocosm experiment monitored for gas emissions and chemical factors. The experiment consisted of combinations of synthetic nitrogen (N), vinasse (V; a liquid waste from ethanol production), and sugarcane-straw blankets. Increases in CO2-C and N2O-N emissions were identified shortly after the addition of both N and V to the soils, thus increasing MB nitrogen (MB-N) and decreasing MB carbon (MB-C) in the N+V-amended soils and altering soil chemical factors that were correlated with the MB. Across 57 soil metagenomic datasets, Actinobacteria (31.5%), Planctomycetes (12.3%), Deltaproteobacteria (12.3%), Alphaproteobacteria (12.0%) and Betaproteobacteria (11.1%) were the most dominant bacterial groups during the experiment. Differences in relative abundance of metagenomic sequences were mainly revealed for Acidobacteria, Actinobacteria, Gammaproteobacteria and Verrucomicrobia with regard to N+V fertilization and straw retention. Differential abundances in bacterial groups were confirmed using 16S rRNA gene-targeted phylum-specific primers for real-time PCR analysis in all soil samples, whose results were in accordance with sequence data, except for Gammaproteobacteria. Actinobacteria were more responsive to straw retention with Rubrobacterales, Bifidobacteriales and Actinomycetales related to the chemical factors of N+V-amended soils. Acidobacteria subgroup 7 and Opitutae, a verrucomicrobial class, were related to the chemical factors of soils without straw retention as a surface blanket. Taken together, the results showed that MB-C and MB-N responded to changes in soil chemical factors and CO2-C and N2O-N emissions, especially for N+V-amended soils. The results also indicated that several taxonomic groups of bacteria, such as Acidobacteria, Actinobacteria and Verrucomicrobia, and their subgroups acted as early-warning indicators of N+V amendments and straw retention in sugarcane-cultivated soils, which can alter the soil chemical factors. ركزت هذه الدراسة على آثار التعديلات العضوية وغير العضوية والاحتفاظ بالقش على الكتلة الحيوية الميكروبية (MB) والمجموعات التصنيفية للبكتيريا في التربة المزروعة بقصب السكر في تجربة عالم متوسط الدفيئة التي تم رصدها لانبعاثات الغازات والعوامل الكيميائية. تألفت التجربة من مزيج من النيتروجين الصناعي (N)، والكرمة (V ؛ نفايات سائلة من إنتاج الإيثانول)، وبطانيات قش قصب السكر. تم تحديد الزيادات في انبعاثات CO2 - C و N2O - N بعد فترة وجيزة من إضافة كل من N و V إلى التربة، وبالتالي زيادة النيتروجين MB (MB - N) وتقليل الكربون MB (MB - C) في التربة المعدلة N+ V وتغيير العوامل الكيميائية للتربة التي كانت مرتبطة مع MB. عبر 57 مجموعة بيانات ميتاجينومية للتربة، كانت البكتيريا الشعاعية (31.5 ٪)، الفطر الخطي (12.3 ٪)، Deltaproteobacteria (12.3 ٪)، Alphaproteobacteria (12.0 ٪) و Betaproteobacteria (11.1 ٪) هي المجموعات البكتيرية الأكثر هيمنة خلال التجربة. تم الكشف عن اختلافات في الوفرة النسبية للتسلسلات الميتاجينومية بشكل أساسي للبكتيريا الحمضية والشعاعية والبروتينية الغاما والميكروبات الثؤلولية فيما يتعلق بتخصيب N+V والاحتفاظ بالقش. تم تأكيد الوفرة التفاضلية في المجموعات البكتيرية باستخدام بادئات محددة للجينات مستهدفة من الحمض النووي الريبوزي 16S لتحليل تفاعل البوليميراز المتسلسل في الوقت الفعلي في جميع عينات التربة، والتي كانت نتائجها وفقًا لبيانات التسلسل، باستثناء جاما بروتيوباكتريا. كانت البكتيريا الشعاعية أكثر استجابة لاحتباس القش باستخدام المطاطوباكتيراليس وبيفيدوباكتيراليس والشعاعية الفطرية المتعلقة بالعوامل الكيميائية للتربة المعدلة N+ V. كانت المجموعة الفرعية 7 من البكتيريا الحمضية و Opitutae، وهي فئة ثؤلولية ميكروبية، مرتبطة بالعوامل الكيميائية للتربة دون احتباس القش كبطانية سطحية. أظهرت النتائج مجتمعة أن MB - C و MB - N استجابت للتغيرات في العوامل الكيميائية للتربة وانبعاثات CO2 - C و N2O - N، خاصة بالنسبة للتربة المعدلة N+ V. كما أشارت النتائج إلى أن العديد من المجموعات التصنيفية للبكتيريا، مثل البكتيريا الحمضية والشعاعية والميكروبات الثؤلولية، ومجموعاتها الفرعية عملت كمؤشرات إنذار مبكر لتعديلات N+V واحتباس القش في التربة المزروعة بقصب السكر، والتي يمكن أن تغير العوامل الكيميائية للتربة.

Abstract Evidence supports various roles for microbial metabolites in the control of multiple aspects of host energy flux including feeding behaviors, digestive efficiency, and energy expenditure, but few studies have quantified the energy utilization of the biomass of the gut microbiota itself. Because gut microbiota exist in an anoxic environment, energy flux is expected to be anaerobic; unfortunately, commonly utilized O2/CO2 respirometry-based approaches are unable to detect anaerobic energy flux. To quantify the contribution of the gut microbial biomass to whole-animal energy flux, we examined the effect of surgical reduction of gut biomass in C57BL/6J mice via cecectomy and assessed energy expenditure using methods sensitive to anaerobic flux, including bomb and direct calorimetry. First, we determined that cecectomy caused an acceleration of weight gain over several months due to a reduction in combined total host plus microbial energy expenditure, as reflected by an increase in energy efficiency (ie, weight gained per calorie absorbed). Second, we determined that under general anesthesia, cecectomy caused immediate changes in heat dissipation that were significantly modified by short-term pretreatment with dietary or pharmaceutical interventions known to modify the microbiome, and confirmed that these effects were undetectable by respirometry. We conclude that while the cecum only contributes approximately 1% of body mass in the mouse, this organ contributes roughly 8% of total resting energy expenditure, that this contribution is predominantly anaerobic, and that the composition and abundance of the cecal microbial contents can significantly alter its contribution to energy flux.

Microbialization refers to the observed shift in ecosystem trophic structure towards higher microbial biomass and energy use. On coral reefs, the proximal causes of microbialization are overfishing and eutrophication, both of which facilitate enhanced growth of fleshy algae, conferring a competitive advantage over calcifying corals and coralline algae. The proposed mechanism for this competitive advantage is the DDAM positive feedback loop (dissolved organic carbon (DOC), disease, algae, microorganism), where DOC released by ungrazed fleshy algae supports copiotrophic, potentially pathogenic bacterial communities, ultimately harming corals and maintaining algal competitive dominance. Using an unprecedented data set of >400 samples from 60 coral reef sites, we show that the central DDAM predictions are consistent across three ocean basins. Reef algal cover is positively correlated with lower concentrations of DOC and higher microbial abundances. On turf and fleshy macroalgal-rich reefs, higher relative abundances of copiotrophic microbial taxa were identified. These microbial communities shift their metabolic potential for carbohydrate degradation from the more energy efficient Embden-Meyerhof-Parnas pathway on coral-dominated reefs to the less efficient Entner-Doudoroff and pentose phosphate pathways on algal-dominated reefs. This 'yield-to-power' switch by microorganism directly threatens reefs via increased hypoxia and greater CO2 release from the microbial respiration of DOC.

A total community DNA sample from an agricultural biogas reactor continuously fed with maize silage, green rye, and small proportions of chicken manure has recently been sequenced using massively parallel pyrosequencing. In this study, the sample was computationally characterized without a prior assembly step, providing quantitative insights into the taxonomic composition and gene content of the underlying microbial community. Clostridiales from the phylum Firmicutes is the most prevalent phylogenetic order, Methanomicrobiales are dominant among methanogenic archaea. An analysis of Operational Taxonomic Units (OTUs) revealed that the entire microbial community is only partially covered by the sequenced sample, despite that estimates suggest only a moderate overall diversity of the community. Furthermore, the results strongly indicate that archaea related to the genus Methanoculleus, using CO2 as electron acceptor and H2 as electron donor, are the main producers of methane in the analyzed biogas reactor sample. A phylogenetic analysis of glycosyl hydrolase protein families suggests that Clostridia play an important role in the digestion of polysaccharides and oligosaccharides. Finally, the results unveiled that most of the organisms constituting the sample are still unexplored.

Seamounts are considered important sources of biodiversity and minerals. However, their biodiversity and health status are not well understood; therefore, potential conservation problems are unknown. The mesophotic reefs of the Vitória-Trindade Seamount Chain (VTC) were investigated via benthic community and fish surveys, metagenomic and water chemistry analyses, and water microbial abundance estimations. The VTC is a mosaic of reef systems and includes fleshy algae dominated rhodolith beds, crustose coralline algae (CCA) reefs, and turf algae dominated rocky reefs of varying health levels. Macro-carnivores and larger fish presented higher biomass at the CCA reefs (4.4 kg per frame) than in the rhodolith beds and rocky reefs (0.0 to 0.1 kg per frame). A larger number of metagenomic sequences identified as primary producers (e.g., Chlorophyta and Streptophyta) were found at the CCA reefs. However, the rocky reefs contained more diseased corals (>90%) than the CCA reefs (~40%) and rhodolith beds (~10%). Metagenomic analyses indicated a heterotrophic and fast-growing microbiome in rocky reef corals that may possibly lead to unhealthy conditions possibly enhanced by environmental features (e.g. light stress and high loads of labile dissolved organic carbon). VTC mounts represent important hotspots of biodiversity that deserve further conservation actions.

ABSTRACT We report on the genome sequences of Lactobacillus vini type strain LMG 23202 T (DSM 20605) (isolated from fermenting grape musts in Spain) and the industrial strain L. vini JP7.8.9 (isolated from a bioethanol plant in northeast Brazil). All contigs were assembled using gsAssembler, and genes were predicted and annotated using Rapid Annotation using Subsystem Technology (RAST). The identified genome sequence of LMG 23202 T had 2.201.333 bp, 37.6% G+C, and 1,833 genes, whereas the identified genome sequence of JP7.8.9 had 2.301.037 bp, 37.8% G+C, and 1,739 genes. The gene repertoire of the species L. vini offers promising opportunities for biotechnological applications.

The health of the coral reefs of the Abrolhos Bank (Southwestern Atlantic) was characterized with a holistic approach using measurements of four ecosystem components: (i) inorganic and organic nutrient concentrations, [1] fish biomass, [1] macroalgal and coral cover and (iv) microbial community composition and abundance. The possible benefits of protection from fishing were particularly evaluated by comparing sites with varying levels of protection. Two reefs within the well-enforced no-take area of the National Marine Park of Abrolhos (Parcel dos Abrolhos and California) were compared with two unprotected coastal reefs (Sebastião Gomes and Pedra de Leste) and one legally protected but poorly enforced coastal reef (the "paper park" of Timbebas Reef). The fish biomass was lower and the fleshy macroalgal cover was higher in the unprotected reefs compared with the protected areas. The unprotected and protected reefs had similar seawater chemistry. Lower vibrio CFU counts were observed in the fully protected area of California Reef. Metagenome analysis showed that the unprotected reefs had a higher abundance of archaeal and viral sequences and more bacterial pathogens, while the protected reefs had a higher abundance of genes related to photosynthesis. Similar to other reef systems in the world, there was evidence that reductions in the biomass of herbivorous fishes and the consequent increase in macroalgal cover in the Abrolhos Bank may be affecting microbial diversity and abundance. Through the integration of different types of ecological data, the present study showed that protection from fishing may lead to greater reef health. The data presented herein suggest that protected coral reefs have higher microbial diversity, with the most degraded reef (Sebastião Gomes) showing a marked reduction in microbial species richness. It is concluded that ecological conditions in unprotected reefs may promote the growth and rapid evolution of opportunistic microbial pathogens.