The year 2020 marked one of the hottest years on record to date, with the average global temperature reaching 1.2 °C above pre-Industrial era (1880) temperatures. Rising temperatures are largely attributed to increasing CO2 levels from the widespread burning of fossil fuels. Terrestrial ecosystems make up the largest global carbon reservoir. In the soil, microorganisms play major roles in carbon and nutrient cycling, decomposition, and mediation of plant health, among several others. Involvement in such important processes makes soil microbial communities incredibly insightful for understanding earth’s changing climate. The Harvard Forests in Petersham, MA implement belowground heating cables to warm experimental soils 5°C above the ambient soil temperature. With this dramatic temperature difference, researchers intended to simulate a worst-case scenario for earth’s climate. However, upward trends in global warming make this projection not as far out of reach as originally thought. In 2017, the heating cables in experimental soil plots were turned off after approximately 15 consecutive years of warming and the soil was allowed to re-equilibrate to the ambient temperature. Experimental soils took around 2 months to reach the same temperature as the control soils. Significant changes in soil respiration levels and moisture were observed, raising the question as to whether soil microbial gene expression levels changed as well. Soil samples were collected for bulk RNA extraction from both heated and control soil plots on the day the heating cables were turned off (Day 0) and sequenced on the Illumina NextSeq platform at the Department of Energy’s Joint Genome Institute. Here I present a metatranscriptomic analysis of the Harvard Forest soil microbiome on Day 0 to uncover the soil microbial community’s transcriptional response to long-term warming. Major phyla that were less transcriptionally active in response to warming include Basidiomycota, Pseudomonadota, Bacteroidetes, and Acidobacteria, which have essential roles in decomposition, nutrient cycling, mediating plant health, and more. Phyla that were more transcriptionally active in response to warming include Actinobacteria, Ascomycota, and Chloroflexota, which participate in biogeochemical cycling, polymer breakdown, antimicrobial activity, and more. These changes in activity reflect the ways in which the soil microbiome responds to chronic warming.

As compostagens abrigam uma grande riqueza microbiológica, englobando populações com distintos requerimentos e tolerâncias fisiológicas que se sucedem ao longo do processo de biodegradação aeróbica da matéria orgânica e que resultam na elevação espontânea de temperatura até 80° C. Com a utilização de abordagens de metagenômica e metatranscritômica, investigamos a composição e a diversidade taxonômica, bem como as funções metabólicas de comunidades microbianas da compostagem termofílica do Parque Zoológico de São Paulo. Foram analisadas amostras em série temporal de duas composteiras (ZC3 e ZC4), as quais exibiram temperaturas entre 50ºC-75ºC ao longo de 99 dias do processo. Verificamos que a degradação de toda a biomassa foi realizada essencialmente por bactérias, e que a estrutura e composição das comunidades microbianas variam ao longo do processo, com elevada abundância relativa das Ordens Clostridiales, Bacillales e Actinomycetales, assim como observado em outros sistemas de compostagem. Entre os organismos abundantes no processo, identificamos unidades taxonômicas operacionais (OTUs) referentes a organismos não-cultiváveis e/ou com genoma ainda desconhecido. O genoma parcial de uma destas OTUs foi reconstruído, a qual provavelmente pertence a um novo gênero da ordem Bacillales. A dinâmica do processo de compostagem foi evidenciada pela variação do número de OTUs e do índice de diversidade filogenética ao longo do tempo, sendo que o início do processo e a fase após a revira apresentaram a maior diversidade. Os resultados indicam que o processo de revira (aeração da massa de composto) impacta fortemente a estrutura e a composição da microbiota e que a desconstrução da biomassa vegetal ocorre de forma sinérgica e sequencial. A variedade de microrganismos e de funções metabólicas ativas na compostagem termofílica reforça o seu potencial de ser uma promissora fonte de bactérias e enzimas termorresistentes úteis em processos industriais. / Composting harbors considerable microbial richness, comprising populations with distinct physiological requirements and tolerances that succeed one another throughout the aerobic biodegradation of the organic matter, resulting in spontaneous temperature rise up to 80° C. Using metagenomic- and metatranscritomic-based approaches, we investigated the composition and taxonomic diversity as well as metabolic functions of microbial communities of a thermophilic composting operation in the São Paulo Zoo Park. We have analyzed time-series samples from two composting cells (ZC3 and ZC4) which exhibited sustained thermophilic profile (50°C-75°C) over 99 days of the process. We found that all biomass degradation was essentially performed by bacteria. The structure and composition of microbial communities vary throughout the process with a high relative abundance of Clostridiales, Bacillales and Actinomycetales, as observed in other composting systems. Among the organisms abundant in the process, we identify Operational Taxonomic Units (OTUs) of uncultivated organisms or with unknown genomes. The partial genome of one of these OTUs was obtained and shown to belong probably to a new genus of Bacillales. Our time-series data showed that the number of OTUs and phylogenetic diversity index changed during composting revealing the dynamics of the process, with the beginning and the stage after turning procedure presenting the highest diverse microbiota. These results indicate that the turning procedure (compost aeration) strongly impacts the microbiota structure and composition and that the deconstruction of the biomass occurs synergistically and sequentially. The huge diversity of microorganisms and metabolic functions active in thermophilic composting strengthen its potential as a promising source of new bacteria and thermostable enzymes that may be helpful in industrial processes.

Arsenic in aquifers poisons more than 100 million people in Asia alone, as aquifers remain the primary source of water for drinking and farming. Previous studies have suggested a link between the mobilisation of arsenic in aquifers and biochemical processes. As a result of the complex interaction of microbes with arsenic bearing minerals, the relatively immobile arsenate [As(V)] is reduced to labile and more soluble arsenite [As(III)] in aquifers, resulting in elevated concentrations of the metalloid. The numerous microbial communities capable of multiple-metabolic activities colonising these arsenic impacted aquifers mean that the exact mechanism of arsenic mobilisation in aquifers remains poorly understood. To resolve this ambiguity, this study undertakes a combination of metaomic, geochemical, and statistical analyses of 75 aqueous and sediment samples (three sample sets) from 3 transects with arsenic impacted aquifers in Bangladesh and Cambodia. Key geochemical and physical properties including arsenic speciation, iron speciation, mineral and elemental compositions, pH and Eh were recorded using the state-of-the art techniques of XANES, XRF, ICP-MS and other in situ techniques. Next generation sequencing (NGS) platforms such as MiSeq, HiSeq, Nextseq and Pyrosequencing, were used to sequence and analyse DNA and RNA extracted from field samples, allowing characterisation the extent bacterial communities, including any arsenic related genes and transcripts found in these arsenic impacted aquifers. The biogeochemical findings suggest that direct As redox transformations are central to arsenic fate and transport, and that there is a residual reactive pool of both As(V) and Fe(III) in deeper sediments that could be released by microbial respiration in response to hydrologic perturbation, such as increased groundwater pumping that introduces reactive organic carbon to depth. The main findings of this molecular investigation are (i) the most abundant bacterial species belonging to the families of Comamonadaceae, Moraxellaceae, Rhodocyclaceae, Gallionellaceae etc, not known for dissimilatory arsenic reduction, might possess arrA genes and thus have the potential to mobilise arsenic through dissimilatory arsenate reduction; (ii) the bacterial community structure revealed through 16S rRNA gene based sequencing and analysis, resembles the family level community structure revealed through the WGS based community analysis; (iii) although arsenic resistant genes are found in many organisms, they are transcribed only in a few organisms; (iv) the application of O2-PLS analyses may be useful for not only identifying novel organisms associated with key biogeochemical process, but also has clear potential to predict the physical/chemical environment in situ associated with microbial samples via community profiling. In conclusion, the results obtained from this study help establish the identity of microorganisms potentially playing a role in arsenic mobilisation in aquifers, and help decipher the underpinning mechanisms. This deeper level of understanding will in turn help to better target measures that can be applied to arsenic mitigation.

As compostagens abrigam uma grande riqueza microbiológica, englobando populações com distintos requerimentos e tolerâncias fisiológicas que se sucedem ao longo do processo de biodegradação aeróbica da matéria orgânica e que resultam na elevação espontânea de temperatura até 80° C. Com a utilização de abordagens de metagenômica e metatranscritômica, investigamos a composição e a diversidade taxonômica, bem como as funções metabólicas de comunidades microbianas da compostagem termofílica do Parque Zoológico de São Paulo. Foram analisadas amostras em série temporal de duas composteiras (ZC3 e ZC4), as quais exibiram temperaturas entre 50ºC-75ºC ao longo de 99 dias do processo. Verificamos que a degradação de toda a biomassa foi realizada essencialmente por bactérias, e que a estrutura e composição das comunidades microbianas variam ao longo do processo, com elevada abundância relativa das Ordens Clostridiales, Bacillales e Actinomycetales, assim como observado em outros sistemas de compostagem. Entre os organismos abundantes no processo, identificamos unidades taxonômicas operacionais (OTUs) referentes a organismos não-cultiváveis e/ou com genoma ainda desconhecido. O genoma parcial de uma destas OTUs foi reconstruído, a qual provavelmente pertence a um novo gênero da ordem Bacillales. A dinâmica do processo de compostagem foi evidenciada pela variação do número de OTUs e do índice de diversidade filogenética ao longo do tempo, sendo que o início do processo e a fase após a revira apresentaram a maior diversidade. Os resultados indicam que o processo de revira (aeração da massa de composto) impacta fortemente a estrutura e a composição da microbiota e que a desconstrução da biomassa vegetal ocorre de forma sinérgica e sequencial. A variedade de microrganismos e de funções metabólicas ativas na compostagem termofílica reforça o seu potencial de ser uma promissora fonte de bactérias e enzimas termorresistentes úteis em processos industriais. / Composting harbors considerable microbial richness, comprising populations with distinct physiological requirements and tolerances that succeed one another throughout the aerobic biodegradation of the organic matter, resulting in spontaneous temperature rise up to 80° C. Using metagenomic- and metatranscritomic-based approaches, we investigated the composition and taxonomic diversity as well as metabolic functions of microbial communities of a thermophilic composting operation in the São Paulo Zoo Park. We have analyzed time-series samples from two composting cells (ZC3 and ZC4) which exhibited sustained thermophilic profile (50°C-75°C) over 99 days of the process. We found that all biomass degradation was essentially performed by bacteria. The structure and composition of microbial communities vary throughout the process with a high relative abundance of Clostridiales, Bacillales and Actinomycetales, as observed in other composting systems. Among the organisms abundant in the process, we identify Operational Taxonomic Units (OTUs) of uncultivated organisms or with unknown genomes. The partial genome of one of these OTUs was obtained and shown to belong probably to a new genus of Bacillales. Our time-series data showed that the number of OTUs and phylogenetic diversity index changed during composting revealing the dynamics of the process, with the beginning and the stage after turning procedure presenting the highest diverse microbiota. These results indicate that the turning procedure (compost aeration) strongly impacts the microbiota structure and composition and that the deconstruction of the biomass occurs synergistically and sequentially. The huge diversity of microorganisms and metabolic functions active in thermophilic composting strengthen its potential as a promising source of new bacteria and thermostable enzymes that may be helpful in industrial processes.

Coral reefs are among the most diverse marine ecosystems, but they are threatened by climate change. The foundation of reef ecosystems is the coral holobiont or metaorganism that consists of the coral animal host, photosynthetic microalgae, bacteria, and viruses (among other organisms). While microalgae provide the energy for corals to build the massive three-dimensional skeletons, bacteria support functions related to metabolism, immunity, and environmental adaptation. Conversely, the function of viruses is less well understood. Although viruses were previously associated with coral disease and bleaching, we are missing an overall understanding of the diversity and identity of viruses associated with corals, in particular for understudied areas such as the Red Sea. Here we characterized coral-associated viral community composition using a large metagenomic and metatransciptomic dataset covering > 1 billion sequences across > 100 coral samples collected from 14 different coral species in the central Red Sea. The viral sequence portion shows that coral species significantly differ from each other, but the most abundant viral families were consistently present. Notably, we found a pervasive abundance of Baculoviridae in metagenomes. In contrast, Polydnaviridae were the most abundant viruses in metatranscriptomes, highlighting that the combined approach of metagenomics and metatranscriptomics is informative with regard to deciphering viral diversity and activity. Our study provides a first comprehensive description of viruses associated with Red Sea corals. In line with previous studies, we confirm the presence of Baculoviridae, Polydnaviridae, Phycodnaviridae, Mimiviridae, and Herpesviridae, which may be considered viral families that are globally and commonly associated with corals. The reason for the pervasive abundance of Baculoviridae in Red Sea corals at present remains unknown, but it is tempting to speculate that the association is related to the uniquely warm and salty environment of the Red Sea.

No description available.

No description available.

Microbial electrochemical technologies (MET) exploit the bioelectrocatalytic activity of microorganisms, with a main focus on waste-to-resource recovery. Electromethanogenesis, a type of MET, describes the process of CO2 reduction specifically to methane, catalyzed by methanogens that utilize the cathode directly as an electron donor or through H2 evolving from the cathode surface. Applications are mainly in the direction of bioelectrochemical power-to-gas, as well as biogas upgrading and carbon capture and utilization. As the cathode and its associated microbial consortia are key to the process, larger scale applications require improvements especially in terms of optimal operational parameters, cathode materials and the dynamics of the effect of electron transfer within the cathodic biofilm. The focus of this dissertation is to improve the understanding of the dynamics and function of methaneproducing biofilms grown on cathodes in electromethanogenic reactors in the presence of two different electron donors: the cathode and the H2 evolving from the cathode surface. The spatial homogeneity of the microbial communities across the area of the cathode was demonstrated, which is relevant for large scale applications where reproducibility is required for predictable engineered systems. Metagenomic and metatranscriptomic methods were applied to elucidate the short-term changes in the actively transcribed methanogenesis and central carbon assimilation pathways in response to varying the availability of electrons by changing the set cathode potential in a novel Methanobacterium species enriched from electromethanogenic biocathodes. Although changes in functional performance were evident with varying potential, no significant differential expression was observed and genes from the methanogenesis and carbon assimilation pathways were highly expressed throughout. Indium tin oxide (ITO) as a potentially hydrogen evolution reaction (HER) – inert cathode material was evaluated using the mixotrophic Methanosarcina barkeri in an attempt to develop a simplified material-science driven approach to future electron transfer studies. It was found to be electrochemically unstable under the tested conditions, losing its conductivity over time. Overall, the findings from these studies provide new knowledge on the effects of electron donor availability on the functional performance and the biocathode community dynamics. The understandings derived from the study are relevant to methanogenic processes and should aid in system scaleup design.

No description available.

Through complex metabolic interactions aquatic microbial life is essential as a driver of ecosystem functions and hence a prerequisite for sustaining plant and animal life in the sea and on Earth. Despite its ecological importance, infor­mation on the complexity of microbial functions and how these are related to environmental conditions is limited. Due to climate change and eutrophication, marine areas facing oxygen depletion are increasing and predicted to continue to do so in the future. Vertically steep oxygen gradients are particularly pronoun­ced in the Baltic Sea. In this thesis, therefore, the ecosystem functions of micro­bial communities were investigated, using metagenomics, to understand how they were distributed along the steep oxygen gradient at the Landsort Deep, the deepest point of the Baltic Sea. Furthermore, microbial communities from the Lands­ort Deep transect were compared to microbial communities of other marine environments to establish whether the environment at this site resulted in a characteristic community. To reveal what microbial community functions and taxa were active in the anoxic sediment a metatranscriptomic approach was used. Results showed a marked effect of the coupled environmental parameters dissolved oxygen, salinity and temperature on distribution of taxa and par­ti­cularly community functions. Microbial communities showed functional capa­cities consistent with a copiotrophic life-style dependent on organic ma­terial sinking through the water column. The eutrophic condition with high organic load was further reflected in the metatranscriptome of the anoxic sedi­ment com­munity, which indicated active carbon mineralisation through ana­erobic hetero­trophic-autotrophic community synergism. New putative linkages between nitro­gen and- sulphur metabolisms were identified at anoxic depths. Further­more, viable Cyanobacteria in the anoxic sediment was evident from the tran­script analyses as another reflection of marine snow. High abundance and expres­­sion of integron integrases were identified as a charac­teristic feature of the Lands­ort Deep communities, and may provide these communities with a mech­an­ism for short-term-adaptation to environmental change. In summary, this thesis clearly documents what impact eutrophication and oxygen depletion have on microbial community functions. Furthermore, it specifically advances the mechanistic insight into microbial processes in anoxic deep-water sediment at both genomic and transcriptional level. Given the predicted progress of oxygen depletion in marine and brackish environments, this work advances information necessary to estimate effects on marine and in particular brackish ecosystem functions where anoxic conditions prevail. / Mikroorganismer är essentiella för fungerande ekosystemfunktioner i akvatiska miljöer och därmed en förutsättning för övrigt växt- och djurliv på vår planet. Trots deras ekologiska nyckelroll är kunskapen om mikroorganismernas funk­tion och komplexitet samt hur dessa är relaterade till miljön begränsad. På grund av eutrofiering och klimatförändringar har marina områden som lider av syrebrist ökat och en ytterligare utbredning av marina och bräckta områden med syrebrist är predicerad i framtiden. Stora områden av Östersjön kännetecknas av vertikala syregradienter med syresatt ytvatten och anoxiskt bottenvatten. I denna avhandling undersöktes därför med metagenomik hur mikrobiella ekosystems funktioner var utbredda längs den vertikala syregradienten i Östersjöns djupaste del, Landsortsdjupet. Dessutom jämfördes de mikrobiella samhällena från Lands­­­ortsdjupet med mikrobiella samhällen från andra marina miljöer för att utröna om den karakteristiska miljön i Landsortsdjupet återspeglade de mikro­biella samhällen som lever där. För att undersöka vilka mikroorganismer samt vilka mikrobiella ekosystemfunktioner som var aktiva i det anoxiska sedimentet i Lands­ortsdjupet användes metatranskriptomik. Resultaten visade en stark kor­re­lation mellan miljöparametrarna syrehalt, salinitet och temperatur och för­del­ningen av mikrobiell taxa och i synnerhet mikrobiell funktion längs Lands­orts­djupets transekt. De mikrobiella samhällena uppvisade en funktionell kapa­citet förenlig med en livsstrategi beroende av organiskt material som sjunker genom vattenkolonnen som en konsekvens av eutrofiering. Eutrofa förhållanden med hög halt av organiskt material var även återspeglad i metatranskriptomet från det anoxiska sedimentet, som indikerade aktiv mineralisering av organiskt kol genom anaerob heterotrof-autotrof synergism. Nya möjliga kopplingar mellan kväve- och svavelmetabolism identifierades i det anoxiska vattnet. Vidare visade resultat från metatranskriptom-analys att livsdugliga cyanobakterier var abun­danta i det mörka och anoxiska sedimentet, vilket även detta kan vara en konse­kvens av sjunkande organiskt material. Hög abundans och hög transkribering av integrongener kunde identifieras som ett karakteristiskt kännetecken hos de mikro­biella samhällena i Landsortsdjupet vilket skulle kunna förse dem med en me­kanism för anpassning till miljöförändringar. Sammanfattningsvis dokumen­terar denna avhandling tydligt vilken påverkan eutrofiering och syrebrist har på mikrobiella funktioner. Dessutom för den specifikt kunskapen om mikrobiella processer i anoxiska djupvattensediment framåt på både genom- och transkrip­tions­nivå. Mot bakgrund av en predicerad ökning av syrebristen i marina mil­jöer, bidrar denna avhandling med information som är viktig för att kunna förutse vilka effekter anoxiska förhållanden kan komma att få på ekosystemfunktioner i marina miljöer och i brackvattenmiljöer i synnerhet.