Polysaccharide degradation potential of bacterial communities in Arctic deep-sea sediments (1200-5500 m water depth)

The majority of the Earth’s surface is covered by fine-grained deep-sea sediments, with bacteria dominating total benthic biomass. These benthic bacterial communities depend on organic matter input from the upper ocean, but as they comprise mostly unknown and uncultivated taxa, we have very limited knowledge of their enzymatic machinery to break down this material. Here we studied deep-sea surface sediments along a seafloor depth gradient from 1000 to 5500 m at the Arctic long-term ecological research station HAUSGARTEN. We applied Illumina 16S rRNA gene surveys based on DNA and cDNA and metagenomic sequencing to elucidate total and active bacterial community composition, and the key functional potentials. Some sequence-dominant taxa of the total community (e.g. members of the Gamma- and Deltaproteobacteria) were underrepresented in the cDNA fraction, while other groups (e.g. Flavobacteriaceae; SAR202 clade) were overrepresented in the active fraction when compared to total community reads. We used the Carbohydrate Active Enzymes database (http://www.cazy.org) to identify protein families in the generated metagenomes, which are associated with polysaccharide degradation, e.g. glycoside hydrolases. We found the same families of glycoside hydrolases in all metagenomes, but their relative contribution to glycoside hydrolase-coding genes varied according to depth. A larger number of hydrolases involved in polysaccharide degradation of algae material (e.g. for laminarin; xylan) was found at shallower depths, while those responsible for the breakdown of bacterial cell walls (e.g. for components of peptidoglycan) were more strongly represented at deep stations. Our findings indicate an adaptation of the communities to differences in organic matter quality

Towards an integrated microbial observatory in the Arctic Ocean

The Fram Strait separates Northeast Greenland from the Svalbard Archipelago, and is the only deep connection to the Arctic Ocean. Therefore, this strait is the only gateway for direct exchange of intermediate and deep waters between the Arctic Ocean and the North Atlantic. Two main currents influence the exchanges: i) the West Spitsbergen Current, bringing Atlantic waters northwards, and ii) the East Greenland Current, which carries cold Arctic waters and ice southwards. These two currents consist of water masses with different origin, generate distinct physical and chemical conditions between the eastern and western parts of the strait, which effects the biological characteristics in this region. Oceanographic observations in the Fram Strait have been carried out for ~15 years with microbial research in the water column focusing mainly on eukaryotes, while very little exploratory work was conducted on pelagic Bacteria and Archaea. Here we present a preliminary report of the first extensive survey across the waters of the Fram Strait focused on Bacterial and Archaeal domains, conducted as part of the Arctic long-term observatory HAUSGARTEN annual expedition in summer 2016. Besides the investigation of “who is out there”, the observations gained in this survey will be integrated with other biological and physical data of the long-term observatory framework and will provide an essential step towards the understanding of the biochemical dynamics in the Fram Strait. In addition, on a long-term plan this project will contribute to the microbial observatory work as part of the FRAM Helmholtz research infrastructure and EU AtlantOS program

Genome size evolution in the Archaea

What determines variation in genome size, gene content and genetic diversity at the broadest scales across the tree of life? Much of the existing work contrasts eukaryotes with prokaryotes, the latter represented mainly by Bacteria. But any general theory of genome evolution must also account for the Archaea, a diverse and ecologically important group of prokaryotes that represent one of the primary domains of cellular life. Here, we survey the extant diversity of Bacteria and Archaea, and ask whether the general principles of genome evolution deduced from the study of Bacteria and eukaryotes also apply to the archaeal domain. Although Bacteria and Archaea share a common prokaryotic genome architecture, the extant diversity of Bacteria appears to be much higher than that of Archaea. Compared with Archaea, Bacteria also show much greater genome-level specialisation to specific ecological niches, including parasitism and endosymbiosis. The reasons for these differences in long-term diversification rates are unclear, but might be related to fundamental differences in informational processing machineries and cell biological features that may favour archaeal diversification in harsher or more energy-limited environments. Finally, phylogenomic analyses suggest that the first Archaea were anaerobic autotrophs that evolved on the early Earth

A concept for international societally relevant microbiology education and microbiology knowledge promulgation in society

Microbes are all pervasive in their distribution and influence on the functioning and well-being of humans, life in general and the planet. Microbially-based technologies contribute hugely to the supply of important goods and services we depend upon, such as the provision of food, medicines and clean water. They also offer mechanisms and strategies to mitigate and solve a wide range of problems and crises facing humanity at all levels, including those encapsulated in the sustainable development goals (SDGs) formulated by the United Nations. For example, microbial technologies can contribute in multiple ways to decarbonisation and hence confronting global warming, provide sanitation and clean water to the billions of people lacking them, improve soil fertility and hence food production and develop vaccines and other medicines to reduce and in some cases eliminate deadly infections. They are the foundation of biotechnology, an increasingly important and growing business sector and source of employment, and the centre of the bioeconomy, Green Deal, etc. But, because microbes are largely invisible, they are not familiar to most people, so opportunities they offer to effectively prevent and solve problems are often missed by decision-makers, with the negative consequences this entrains. To correct this lack of vital knowledge, the International Microbiology Literacy Initiative–the IMiLI–is recruiting from the global microbiology community and making freely available, teaching resources for a curriculum in societally relevant microbiology that can be used at all levels of learning. Its goal is the development of a society that is literate in relevant microbiology and, as a consequence, able to take full advantage of the potential of microbes and minimise the consequences of their negative activities. In addition to teaching about microbes, almost every lesson discusses the influence they have on sustainability and the SDGs and their ability to solve pressing problems of societal inequalities. The curriculum thus teaches about sustainability, societal needs and global citizenship. The lessons also reveal the impacts microbes and their activities have on our daily lives at the personal, family, community, national and global levels and their relevance for decisions at all levels. And, because effective, evidence-based decisions require not only relevant information but also critical and systems thinking, the resources also teach about these key generic aspects of deliberation. The IMiLI teaching resources are learner-centric, not academic microbiology-centric and deal with the microbiology of everyday issues. These span topics as diverse as owning and caring for a companion animal, the vast range of everyday foods that are produced via microbial processes, impressive geological formations created by microbes, childhood illnesses and how they are managed and how to reduce waste and pollution. They also leverage the exceptional excitement of exploration and discovery that typifies much progress in microbiology to capture the interest, inspire and motivate educators and learners alike. The IMiLI is establishing Regional Centres to translate the teaching resources into regional languages and adapt them to regional cultures, and to promote their use and assist educators employing them. Two of these are now operational. The Regional Centres constitute the interface between resource creators and educators–learners. As such, they will collect and analyse feedback from the end-users and transmit this to the resource creators so that teaching materials can be improved and refined, and new resources added in response to demand: educators and learners will thereby be directly involved in evolution of the teaching resources. The interactions between educators–learners and resource creators mediated by the Regional Centres will establish dynamic and synergistic relationships–a global societally relevant microbiology education ecosystem–in which creators also become learners, teaching resources are optimised and all players/stakeholders are empowered and their motivation increased. The IMiLI concept thus embraces the principle of teaching societally relevant microbiology embedded in the wider context of societal, biosphere and planetary needs, inequalities, the range of crises that confront us and the need for improved decisioning, which should ultimately lead to better citizenship and a humanity that is more sustainable and resilient. The biosphere of planet Earth is a microbial world: a vast reactor of countless microbially driven chemical transformations and energy transfers that push and pull many planetary geochemical processes, including the cycling of the elements of life, mitigate or amplify climate change (e.g., Nature Reviews Microbiology, 2019, 17, 569) and impact the well-being and activities of all organisms, including humans. Microbes are both our ancestors and creators of the planetary chemistry that allowed us to evolve (e.g., Life's engines: How microbes made earth habitable, 2023). To understand how the biosphere functions, how humans can influence its development and live more sustainably with the other organisms sharing it, we need to understand the microbes. In a recent editorial (Environmental Microbiology, 2019, 21, 1513), we advocated for improved microbiology literacy in society. Our concept of microbiology literacy is not based on knowledge of the academic subject of microbiology, with its multitude of component topics, plus the growing number of additional topics from other disciplines that become vitally important elements of current microbiology. Rather it is focused on microbial activities that impact us–individuals/communities/nations/the human world–and the biosphere and that are key to reaching informed decisions on a multitude of issues that regularly confront us, ranging from personal issues to crises of global importance. In other words, it is knowledge and understanding essential for adulthood and the transition to it, knowledge and understanding that must be acquired early in life in school. The 2019 Editorial marked the launch of the International Microbiology Literacy Initiative, the IMiLI. HERE, WE PRESENT our concept of how microbiology literacy may be achieved and the rationale underpinning it; the type of teaching resources being created to realise the concept and the framing of microbial activities treated in these resources in the context of sustainability, societal needs and responsibilities and decision-making; and the key role of Regional Centres that will translate the teaching resources into local languages, adapt them according to local cultural needs, interface with regional educators and develop and serve as hubs of microbiology literacy education networks. The topics featuring in teaching resources are learner-centric and have been selected for their inherent relevance, interest and ability to excite and engage. Importantly, the resources coherently integrate and emphasise the overarching issues of sustainability, stewardship and critical thinking and the pervasive interdependencies of processes. More broadly, the concept emphasises how the multifarious applications of microbial activities can be leveraged to promote human/animal, plant, environmental and planetary health, improve social equity, alleviate humanitarian deficits and causes of conflicts among peoples and increase understanding between peoples (Microbial Biotechnology, 2023, 16(6), 1091–1111). Importantly, although the primary target of the freely available (CC BY-NC 4.0) IMiLI teaching resources is schoolchildren and their educators, they and the teaching philosophy are intended for all ages, abilities and cultural spectra of learners worldwide: in university education, lifelong learning, curiosity-driven, web-based knowledge acquisition and public outreach. The IMiLI teaching resources aim to promote development of a global microbiology education ecosystem that democratises microbiology knowledge.http://www.wileyonlinelibrary.com/journal/mbt2hj2024BiochemistryGeneticsMicrobiology and Plant PathologySDG-01:No povertySDG-02:Zero HungerSDG-03:Good heatlh and well-beingSDG-04:Quality EducationSDG-06:Clean water and sanitationSDG-07:Affordable and clean energySDG-08:Decent work and economic growthSDG-12:Responsible consumption and productionSDG-13:Climate actionSDG-14:Life below wate

Effet de la mycorhization sur la structure génétique et fonctionnelle des communautés bactériennes dans la rhizosphère de <em>Medicago truncatula</em>

Bacterial communities associated with (i) M. Truncatula J5 (Myc+/Nod+) and TRV48 (Myc+/Nod-), and with (ii) M. Truncatula TRV25 (Myc-/Nod-) were compared. The genetic structure of communities was characterized with an A-RISA DNA fingerprint. The genetic structures of communities associated with mycorrhizal and non-mycorrhizal roots were significantly different. Bacteria belonging to the Oxalobacteraceae and Comamonadaceae families were preferentially associated with mycorrhizal roots. The genetic diversity of cultured bacteria belonging to these groups was analysed by BOX-PCR. The diversity of isolates from mycorrhizal and non-mycorrhizal roots was significantly different. The functionality of communities was assessed by a proteomic approach. Proteins involved in structural stabilisation were more frequent in the metaproteome of communities associated with mycorrhizal roots suggesting bacteria colonising mycorrhizal roots might experience greater stress than those colonising non-mycorrhizal roots.Les communautés bactériennes associées à (i) M. Truncatula J5 (Myc+/Nod+) et TRV48 (Myc+/Nod-) et à (ii) M. Truncatula TRV25 (Myc-/Nod-) ont été comparées. La structure génétique des communautés a été caractérisée par une empreinte moléculaire A-RISA. Les structures génétiques des communautés associées aux racines mycorhizées et non-mycorhizées étaient significativement différentes. Des bactéries appartenant aux Oxalobacteraceae et aux Comamonadaceae étaient préférentiellement associées aux racines mycorhizées. La diversité génétique des bactéries cultivables appartenant à ces groupes a été analysée par BOX-PCR. La diversité des isolats issus des racines mycorhizées et non-mycorhizées était significativement différente. La structure fonctionnelle des communautés a été caractérisée par une approche protéomique. Des protéines impliquées dans la stabilisation structurelle étaient significativement plus fréquentes dans le métaprotéome des communautés associées aux racines mycorhizées suggérant que les bactéries colonisant les racines mycorhizées subissent un stress plus élevé que celles colonisant les racines non-mycorhizées

Towards a systematic understanding of differences between archaeal and bacterial diversity

In this crystal ball, we discuss emerging methodologies that can help reaching a synthesis on the biodiversity of Archaea and Bacteria and thereby inform a central enigma in microbiology, i.e. the fundamental split between these primary domains of life and the apparent lower diversity of the Archaea

Effet de la mycorhization sur la structure génétique et fonctionnelle des communautés bactériennes dans la rhizosphère de Medicago truncatula

Les communautés bactériennes associées à (i) M. truncatula J5 (Myc+/Nod+) et TRV48 (Myc+/Nod-) et à (ii) M. truncatula TRV25 (Myc-/Nod-) ont été comparées. La structure génétique des communautés a été caractérisée par une empreinte moléculaire A-RISA. Les structures génétiques des communautés associées aux racines mycorhizées et non-mycorhizées étaient significativement différentes. Des bactéries appartenant aux Oxalobacteraceae et aux Comamonadaceae étaient préférentiellement associées aux racines mycorhizées. La diversité génétique des bactéries cultivables appartenant à ces groupes a été analysée par BOX-PCR. La diversité des isolats issus des racines mycorhizées et non-mycorhizées était significativement différente. La structure fonctionnelle des communautés a été caractérisée par une approche protéomique. Des protéines impliquées dans la stabilisation structurelle étaient significativement plus fréquentes dans le métaprotéome des communautés associées aux racines mycorhizées suggérant que les bactéries colonisant les racines mycorhizées subissent un stress plus élevé que celles colonisant les racines non-mycorhizées.Bacterial communities associated with (i) M. truncatula J5 (Myc+/Nod+) and TRV48 (Myc+/Nod-), and with (ii) M. truncatula TRV25 (Myc-/Nod-) were compared. The genetic structure of communities was characterized with an A-RISA DNA fingerprint. The genetic structures of communities associated with mycorrhizal and non-mycorrhizal roots were significantly different. Bacteria belonging to the Oxalobacteraceae and Comamonadaceae families were preferentially associated with mycorrhizal roots. The genetic diversity of cultured bacteria belonging to these groups was analysed by BOX-PCR. The diversity of isolates from mycorrhizal and non-mycorrhizal roots was significantly different. The functionality of communities was assessed by a proteomic approach. Proteins involved in structural stabilisation were more frequent in the metaproteome of communities associated with mycorrhizal roots suggesting bacteria colonising mycorrhizal roots might experience greater stress than those colonising non-mycorrhizal roots.DIJON-BU Sciences Economie (212312102) / SudocSudocFranceF

Diversity of hydrolytic enzymes among Arctic deep-sea sediment bacteria

The vast majority of deep-sea ecosystems are sustained by exported organic material from the productive, sunlit surface ocean. Bacteria dominate benthic communities both in biomass and abundance, and have been recognized as the key players in the remineralization of organic material. Since most sediment bacteria remain however uncultivated and represent unknown taxa, we have very limited knowledge of their metabolic capabilities and enzymatic machinery. Here we studied deep-sea surface sediments along a seafloor depth gradient from 1200 m to 5500 m at the Arctic long-term ecological research station HAUSGARTEN. We applied Illumina 16S rRNA gene surveys based on DNA and cDNA, as well as metagenomic and -transcriptomic sequencing to elucidate total and active bacterial community composition and gain insight into the carbohydrate processing and uptake capabilities of deep-sea benthic bacteria. We identified specific taxa of interest and quantified their cellular abundance using CAtalyzed Reporter Deposition–Fluorescence In Situ Hybridization. Results from the different molecular approaches were in good agreement and suggested similar community structures with the same dominant members. Interestingly, typically predominant sediment taxa, i.e. the JTB255 marine group, the Sh765B.TzT29 group or the OM1 clade, were underrepresented in the active part of the community, while other usually low-abundant taxa, i.e. Flavobacteriia and the SAR202 clade, were overrepresented. At low taxonomic resolution, communities along the slope were similar, yet showed high turnover at species level. Although, the repertoire of carbohydrate-active enzymes (e.g. polysaccharide hydrolases) appeared unchanging along the depth gradient, the relative contribution of distinct enzyme-coding genes varied. Specific glycoside hydrolases involved in polysaccharide degradation of algae material (e.g. for laminarin; xylan) had higher counts at shallow depth, while others responsible for the breakdown of bacterial cell walls (e.g. for components of peptidoglycan) were more strongly represented at deep stations. Our findings indicate an adaptation of the communities to differences in organic matter quality

PacificOcean_140m_contigs.fa

Complete assembly of the Tara Oceans metagenome (SRA accession: ERR599156). Metagenome was derived from Pacific Ocean sampled at 140m depth. See the associated publication for technical details

alphaproteobacteria_untreated.aln

Concatenated supermatrix alignment of 72 genes conserved among alphaproteobacteria. See associated publication for technical details on how this alignment was prepared