150 research outputs found
Evolutionary diversification of methanotrophic ANME-1 archaea and their expansive virome
No full textANME-1 archaea are important because of their ability to metabolize methane through anaerobic oxidation. Here the authors use metagenomics on hydrothermal samples from the Gulf of California to characterize a family of ANME-1 and its virome. 'Candidatus Methanophagales' (ANME-1) is an order-level clade of archaea responsible for anaerobic methane oxidation in deep-sea sediments. The diversity, ecology and evolution of ANME-1 remain poorly understood. In this study, we use metagenomics on deep-sea hydrothermal samples to expand ANME-1 diversity and uncover the effect of virus-host dynamics. Phylogenetic analyses reveal a deep-branching, thermophilic family, 'Candidatus Methanospirareceae', closely related to short-chain alkane oxidizers. Global phylogeny and near-complete genomes show that hydrogen metabolism within ANME-1 is an ancient trait that was vertically inherited but differentially lost during lineage diversification. Metagenomics also uncovered 16 undescribed virus families so far exclusively targeting ANME-1 archaea, showing unique structural and replicative signatures. The expansive ANME-1 virome contains a metabolic gene repertoire that can influence host ecology and evolution through virus-mediated gene displacement. Our results suggest an evolutionary continuum between anaerobic methane and short-chain alkane oxidizers and underscore the effects of viruses on the dynamics and evolution of methane-driven ecosystems
NAP to EVRS: a re-evaluation of the Dutch input and its impact on the realization of the European Vertical Reference System
No full textDouble degree of Master of Science in Applied Geophysics at Delft University of Technology, ETH Zürich and RWTH Aachen University. - In 2004, Rijkswaterstaat provided geopotential differences between the benchmarks of the Normaal Amsterdams Peil (NAP) network to the Bundesamt für Kartographie und Geodäsie (BKG) for the realization of the European Vertical Reference System (EVRS). This data was found to be incorrect, resulting in inaccurate transformations between EVRF2007 and the national height systems of the participating countries. To correct the realization of the EVRS and obtain accurate transformations between the height systems, it is essential that the BKG is provided with correct geopotential information on the NAP network. In this thesis, a computational procedure has been developed to obtain correct geopotential differences. The final procedure was implemented in a MATLAB software package that was provided to Rijkswaterstaat for future computations. The old results were compared with the newly computed results, in order to obtain insight into the origin of the errors made in 2004. The impact of these errors on realizations of the EVRS was examined as well. Finally, the connection of the NAP levelling network to the neighbouring countries, and thus the Unified European Levelling Network, (UELN) was investigated. Due to the available data, most steps in the computational procedure were already predefined. Therefore, the main development was a method for predicting gravity at the levelling benchmarks. Observed gravity was reduced to surface gravity anomalies to remove height dependency. This makes accurate 2-D interpolation possible. Four methods were tested for the interpolation of these gravity anomalies: ordinary Kriging, least-squares collocation, cubic spline and biharmonic spline. Biharmonic spline interpolation was selected as the gravity prediction method for the final procedure. For potentially further improvement of the gravity prediction, two gravity corrections were investigated as well: residual terrain modelling and correcting for a global gravity field model. Both corrections were found to cause negligible improvement to the gravity prediction with respect to the uncertainty of the levelling observations. Therefore, these corrections were not used in the final procedure. Large regional differences were observed between the newly obtained results and those of Rijkswaterstaat. These differences could predominantly be explained by a mistake in sign convention of the surface gravity anomalies when restoring the observed gravity. In an updated realization of the EVRS, using the new NAP geopotential information, a tilt of several millimetres within the Netherlands and Belgium is observed. When updated data from other countries are also considered, datum points heights varied in the centimetre range. Finally, there are a total of 28 Dutch-German cross-border observations at 13 locations, evenly distributed along the border. This lead to the conclusion that the connection between the NAP and the German levelling network is strong. The connection of the NAP with the Belgian network is much weaker, with only a single observation currently known at the BKG. Although, from the data used here it seems that more connections should be readily available.Civil Engineering and GeosciencesGeoscience and Remote SensingApplied Geophysics and Civil Engineerin
PALSAR InSAR Processing, Subsidence of agricultural highland regions in Yemen
No full textThe use of Interferometric Synthetic Aperture Radar (InSAR) to monitor ground subsidence and the general principles behind InSAR were studied and summarized. The obtained knowledge was used to process the Phased Array type L-band Synthetic Aperture Radar (PALSAR) data of the region between Sana’a and Dhamar, Yemen, from raw data to interferograms. During this processing unwrapping proved to be a difficult procedure creating phase jumps. This problem can increased in size when using wrong mask. After unwrapping in the best possible way and filtering the result, three basins turned out to subside with high rates. The biggest basin at an average maximum rate of 32 cm?yr and the smaller basin with an average maximum rate of 53 cm?yr. This subsidence is not linear during the year, in the summer subsidence is faster than during the winter.Applied Earth ScienceGeoscience & EngineeringCivil Engineering and Geoscience
Metabolic marker gene mining provides insight in global mcrA diversity and, coupled with targeted genome reconstruction, sheds further light on metabolic potential of the Methanomassiliicoccales
No full textOver the past years, metagenomics has revolutionized our view of microbial diversity. Moreover, extracting near-complete genomes from metagenomes has led to the discovery of known metabolic traits in unsuspected lineages. Genome-resolved metagenomics relies on assembly of the sequencing reads and subsequent binning of assembled contigs, which might be hampered by strain heterogeneity or low abundance of a target organism. Here we present a complementary approach, metagenome marker gene mining, and use it to assess the global diversity of archaeal methane metabolism through the mcrA gene. To this end, we have screened 18,465 metagenomes for the presence of reads matching a database representative of all known mcrA proteins and reconstructed gene sequences from the matching reads. We use our mcrA dataset to assess the environmental distribution of the Methanomassiliicoccales and reconstruct and analyze a draft genome belonging to the ‘Lake Pavin cluster’, an uncultivated environmental clade of the Methanomassiliicoccales. Analysis of the ‘Lake Pavin cluster’ draft genome suggests that this organism has a more restricted capacity for hydrogenotrophic methylotrophic methanogenesis than previously studied Methanomassiliicoccales, with only genes for growth on methanol present. However, the presence of the soluble subunits of methyltetrahydromethanopterin:CoM methyltransferase (mtrAH) provide hypothetical pathways for methanol fermentation, and aceticlastic methanogenesis that await experimental verification. Thus, we show that marker gene mining can enhance the discovery power of metagenomics, by identifying novel lineages and aiding selection of targets for in-depth analyses. Marker gene mining is less sensitive to strain heterogeneity and has a lower abundance threshold than genome-resolved metagenomics, as it only requires short contigs and there is no binning step. Additionally, it is computationally cheaper than genome resolved metagenomics, since only a small subset of reads needs to be assembled. It is therefore a suitable approach to extract knowledge from the many publicly available sequencing projects
Metabolic marker gene mining provides insight in global mcrA diversity and, coupled with targeted genome reconstruction, sheds light on metabolic versatility of the<i>Methanomassiliicoccales</i>
No full textAbstractOver the past years, metagenomics has revolutionized our view of microbial diversity. Moreover, extracting near-complete genomes from metagenomes has led to the discovery of known metabolic traits in unsuspected lineages. Genome-resolved metagenomics relies on assembly of the sequencing reads and subsequent binning of assembled contigs, which might be hampered by strain heterogeneity or low abundance of a target organism. Here we present a complementary approach, metagenome marker gene mining, and use it to assess the global diversity of archaeal methane metabolism through the mcrA gene. To this end, we have screened 18,465 metagenomes for the presence of reads matching a database representative of all known mcrA proteins and reconstructed gene sequences from the matching reads. We use our mcrA dataset to assess the environmental distribution of theMethanomassiliicoccalesand reconstruct and analyze a draft genome belonging to the ‘Lake Pavin cluster’, an understudied environmental clade of theMethanomassiliicoccales. Thus, we show that marker gene mining can enhance the discovery power of metagenomics, by identifying novel lineages and aiding selection of targets for in-depth analyses. Marker gene mining is less sensitive to strain heterogeneity and has a lower abundance threshold than genome-resolved metagenomics, as it only requires short contigs and there is no binning step. Additionally, it is computationally cheaper than genome resolved metagenomics, since only a small subset of reads needs to be assembled. It is therefore a suitable approach to extract knowledge from the many publicly available sequencing projects.</jats:p
ASM-Clust: classifying functionally diverse protein families using alignment score matrices
No full textRapid advances in sequencing technology have resulted in the availability of genomes from organisms across the tree of life. Accurately interpreting the function of proteins in these genomes is a major challenge, as annotation transfer based on homology frequently results in misannotation and error propagation. This challenge is especially pressing for organisms whose genomes are directly obtained from environmental samples, as interpretation of their physiology and ecology is often based solely on the genome sequence. For complex protein (super)families containing a large number of sequences, classification can be used to determine whether annotation transfer is appropriate, or whether experimental evidence for function is lacking. Here we present a novel computational approach for de novo classification of large protein (super)families, based on clustering an alignment score matrix obtained by aligning all sequences in the family to a small subset of the data. We evaluate our approach on the enolase family in the Structure Function Linkage Database
Metagenomic analysis of nitrogen and methane cycling in the Arabian Sea oxygen minimum zone
No full textOxygen minimum zones (OMZ) are areas in the global ocean where oxygen concentrations drop to below one percent. Low oxygen concentrations allow alternative respiration with nitrate and nitrite as electron acceptor to become prevalent in these areas, making them main contributors to oceanic nitrogen loss. The contribution of anammox and denitrification to nitrogen loss seems to vary in different OMZs. In the Arabian Sea, both processes were reported. Here, we performed a metagenomics study of the upper and core zone of the Arabian Sea OMZ, to provide a comprehensive overview of the genetic potential for nitrogen and methane cycling. We propose that aerobic ammonium oxidation is carried out by a diverse community of Thaumarchaeota in the upper zone of the OMZ, whereas a low diversity of Scalindua-like anammox bacteria contribute significantly to nitrogen loss in the core zone. Aerobic nitrite oxidation in the OMZ seems to be performed by Nitrospina spp. and a novel lineage of nitrite oxidizing organisms that is present in roughly equal abundance as Nitrospina. Dissimilatory nitrate reduction to ammonia (DNRA) can be carried out by yet unknown microorganisms harbouring a divergent nrfA gene. The metagenomes do not provide conclusive evidence for active methane cycling; however, a low abundance of novel alkane monooxygenase diversity was detected. Taken together, our approach confirmed the genomic potential for an active nitrogen cycle in the Arabian Sea and allowed detection of hitherto overlooked lineages of carbon and nitrogen cycle bacteria
Genome-based microbial ecology of anammox granules in a full-scale wastewater treatment system
No full textPartial-nitritation anammox (PNA) is a novel wastewater treatment procedure for energy-efficient ammonium removal. Here we use genome-resolved metagenomics to build a genome-based ecological model of the microbial community in a full-scale PNA reactor. Sludge from the bioreactor examined here is used to seed reactors in wastewater treatment plants around the world; however, the role of most of its microbial community in ammonium removal remains unknown. Our analysis yielded 23 near-complete draft genomes that together represent the majority of the microbial community. We assign these genomes to distinct anaerobic and aerobic microbial communities. In the aerobic community, nitrifying organisms and heterotrophs predominate. In the anaerobic community, widespread potential for partial denitrification suggests a nitrite loop increases treatment efficiency. Of our genomes, 19 have no previously cultivated or sequenced close relatives and six belong to bacterial phyla without any cultivated members, including the most complete Omnitrophica (formerly OP3) genome to date.BT/Environmental Biotechnolog
Community Structure and Microbial Associations in Sediment-Free Methanotrophic Enrichment Cultures from a Marine Methane Seep
No full textSyntrophic consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB) consume large amounts of methane and serve as the foundational microorganisms in marine methane seeps. Despite their importance in the carbon cycle, research on the physiology of ANME-SRB consortia has been hampered by the slow growth and complex physicochemical environment the consortia inhabit. Here, we report successful sediment-free enrichment of ANME-SRB consortia from deep-sea methane seep sediments in the Santa Monica Basin, California. Anoxic Percoll density gradients and size-selective filtration were used to separate ANME-SRB consortia from sediment particles and single cells to accelerate the cultivation process. Over a 3-year period, a subset of the sediment-associated ANME and SRB lineages, predominantly comprised of ANME-2a/2b (“Candidatus Methanocomedenaceae”) and their syntrophic bacterial partners, SEEP-SRB1/2, adapted and grew under defined laboratory conditions. Metagenome-assembled genomes from several enrichments revealed that ANME-2a, SEEP-SRB1, and Methanococcoides in different enrichments from the same inoculum represented distinct species, whereas other coenriched microorganisms were closely related at the species level. This suggests that ANME, SRB, and Methanococcoides are more genetically diverse than other members in methane seeps. Flow cytometry sorting and sequencing of cell aggregates revealed that Methanococcoides, Anaerolineales, and SEEP-SRB1 were overrepresented in multiple ANME-2a cell aggregates relative to the bulk metagenomes, suggesting they were physically associated and possibly interacting. Overall, this study represents a successful case of selective cultivation of anaerobic slow-growing microorganisms from sediments based on their physical characteristics, introducing new opportunities for detailed genomic, physiological, biochemical, and ecological analyses. IMPORTANCE Biological anaerobic oxidation of methane (AOM) coupled with sulfate reduction represents a large methane sink in global ocean sediments. Methane consumption is carried out by syntrophic archaeal-bacterial consortia and fuels a unique ecosystem, yet the interactions in these slow-growing syntrophic consortia and with other associated community members remain poorly understood. The significance of this study is the establishment of sediment-free enrichment cultures of anaerobic methanotrophic archaea and sulfate-reducing bacteria performing AOM with sulfate using selective cultivation approaches based on size, density, and metabolism. By reconstructing microbial genomes and analyzing community composition of the enrichment cultures and cell aggregates, we shed light on the diversity of microorganisms physically associated with AOM consortia beyond the core syntrophic partners. These enrichment cultures offer simplified model systems to extend our understanding of the diversity of microbial interactions within marine methane seeps
Shotgun metagenomic data reveals signifcant abundance but low diversity of Candidatus Scalindua marine anammox bacteria in the Arabian Sea oxygen minimum zone
No full textAnaerobic ammonium oxidizing (anammox) bacteria are responsible for a significant portion of the loss of fixed nitrogen from the oceans, making them important players in the global nitrogen cycle. To date, marine anammox bacteria found in both water columns and sediments worldwide belong almost exclusively to Candidatus Scalindua species. Recently the genome assembly of a marine anammox enrichment culture dominated by Candidatus Scalindua profunda became available and can now be used as a template to study metagenome data obtained from various oxygen minimum zones. Here, we sequenced genomic DNA from suspended particulate matter recovered at the upper (170 m deep) and center (600 m) area of the oxygen minimum zone in the Arabian Sea by SOLiD and Ion Torrent technology. The genome of Candidatus Scalindua profunda served as a template to collect reads. Based on the mapped reads marine anammox Abundance was estimated to be at least 0.4% in the upper and 1.7% in the center area. Single nucleotide variation (SNV) analysis was performed to assess diversity of the Candidatus Scalindua populations. Most highly covered were the two diagnostic anammox genes hydrazine synthase (scal_01318c, hzsA) and hydrazine dehydrogenase (scal_03295, hdh), while other genes involved in anammox metabolism (narGH, nirS, amtB, focA and ACS) had a lower coverage but could still be assembled and analyzed. The results show that Candidatus Scalindua is abundantly present in the Arabian Sea OMZ, but that the diversity within the ecosystem is relatively low
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