scholarly journals Genomic profiling ofNitrospiraspecies reveals ecological success of comammoxNitrospira

2019 ◽  
Author(s):  
Alejandro Palomo ◽  
Arnaud Dechesne ◽  
Barth F. Smets
Keyword(s):  
Large Scale ◽  
Wastewater Treatment Plants ◽  
Phylogenetic Signal ◽  
Environmental Filtering ◽  
Genomic Diversity ◽  
Metagenomic Data ◽  
Hydroxylamine Oxidoreductase ◽  
Environmental Distribution ◽  
Genome Database ◽  
Ecological Success

AbstractNitrification was long thought to consist in the stepwise oxidation of ammonia to nitrite and of nitrite to nitrate by ammonia oxidizing and nitrite oxidizing microorganisms, respectively. Recently, single microorganisms capable of complete ammonia to nitrate oxidation (comammox) were identified in theNitrospiragenus. This genus, previously considered to only contain canonical nitrite oxidizers is diverse and has a broad environmental distribution. Yet, a global insight into the abundance, niche preference, and genomic diversity ofNitrospirais missing. Here, we established the largestNitrospiragenome database to date, revealing 68 putative species, most without cultivated representatives. We performed a global survey through read recruitment of metagenomic data from various environments against this database that identified that environmental filtering structures species distribution, without large scale biogeographical signal. The ecological success of comammoxNitrospirais evident as they outnumber and are more diverse than canonicalNitrospirain communities from all environments but wastewater treatment plants. We detect a phylogenetic signal inNitrospiraspecies habitat preference, that is strongest for canonicalNitrospiraspecies. ComammoxNitrospiraeco-evolutionary history is more complex with subclades achieving rapid niche divergence via horizontal transfer of genes, including that encoding the hydroxylamine oxidoreductase, one of the key enzymes involved in nitrification.

Bottlenecks in the Implementation of On-Site Wastewater Treatment Plants on a Large Scale in The Netherlands

1990 ◽  
Vol 22 (3-4) ◽  
pp. 291-298
Author(s):  
Frits A. Fastenau ◽  
Jaap H. J. M. van der Graaf ◽  
Gerard Martijnse
Keyword(s):  
Wastewater Treatment ◽  
The Netherlands ◽  
Large Scale ◽  
Wastewater Treatment Plants ◽  
Housing Stock ◽  
Research Work ◽  
Field Research ◽  
Domestic Wastewater ◽  
Research Programme ◽  
Definition Of

More than 95 % of the total housing stock in the Netherlands is connected to central sewerage systems and in most cases the wastewater is treated biologically. As connection to central sewerage systems has reached its economic limits, interest in on-site treatment of the domestic wastewater of the remaining premises is increasing. A large scale research programme into on-site wastewater treatment up to population equivalents of 200 persons has therefore been initiated by the Dutch Ministry of Housing, Physical Planning and Environment. Intensive field-research work did establish that the technological features of most on-site biological treatment systems were satisfactory. A large scale implementation of these systems is however obstructed in different extents by problems of an organisational, financial and/or juridical nature and management difficulties. At present research is carried out to identify these bottlenecks and to analyse possible solutions. Some preliminary results are given which involve the following ‘bottlenecks':-legislation: absence of co-ordination and absence of a definition of ‘surface water';-absence of subsidies;-ownership: divisions in task-setting of Municipalities and Waterboards; divisions involved with cost-sharing;-inspection; operational control and maintenance; organisation of management;-discharge permits;-pollution levy;-sludge disposal. Final decisions and practical elaboration of policies towards on-site treatment will have to be formulated in a broad discussion with all the authorities and interest groups involved.

Analysis and design of suitable model structures for activated sludge tanks with circulating flow

1999 ◽  
Vol 39 (4) ◽  
pp. 55-60 ◽  
Author(s):  
J. Alex ◽  
R. Tschepetzki ◽  
U. Jumar ◽  
F. Obenaus ◽  
K.-H. Rosenwinkel
Keyword(s):  
Activated Sludge ◽  
Large Scale ◽  
Wastewater Treatment Plants ◽  
Treatment Plant ◽  
High Sensitivity ◽  
Suitable Model ◽  
Model Structure ◽  
Analysis And Design ◽  
Hydraulic Behaviour ◽  
Model Structures

Activated sludge models are widely used for planning and optimisation of wastewater treatment plants and on line applications are under development to support the operation of complex treatment plants. A proper model is crucial for all of these applications. The task of parameter calibration is focused in several papers and applications. An essential precondition for this task is an appropriately defined model structure, which is often given much less attention. Different model structures for a large scale treatment plant with circulation flow are discussed in this paper. A more systematic method to derive a suitable model structure is applied to this case. Results of a numerical hydraulic model are used for this purpose. The importance of these efforts are proven by a high sensitivity of the simulation results with respect to the selection of the model structure and the hydraulic conditions. Finally it is shown, that model calibration was possible only by adjusting to the hydraulic behaviour and without any changes of biological parameters.

scholarly journals IGD: high-performance search for large-scale genomic interval datasets

2020 ◽  
Author(s):  
Jianglin Feng ◽  
Nathan C Sheffield
Keyword(s):  
High Performance ◽  
Large Scale ◽  
Interval Data ◽  
Scale Analysis ◽  
Genome Database ◽  
Genomic Interval ◽  
Critical Resource ◽  
Genomic Regions ◽  
Genome Projects

Abstract Summary Databases of large-scale genome projects now contain thousands of genomic interval datasets. These data are a critical resource for understanding the function of DNA. However, our ability to examine and integrate interval data of this scale is limited. Here, we introduce the integrated genome database (IGD), a method and tool for searching genome interval datasets more than three orders of magnitude faster than existing approaches, while using only one hundredth of the memory. IGD uses a novel linear binning method that allows us to scale analysis to billions of genomic regions. Availability https://github.com/databio/IGD

scholarly journals Co-occurrences of tropical trees in eastern South America: disentangling abiotic and biotic forces

Plant Ecology ◽  
2021 ◽  
Author(s):  
Emma-Liina Marjakangas ◽  
Otso Ovaskainen ◽  
Nerea Abrego ◽  
Vidar Grøtan ◽  
Alexandre A. de Oliveira ◽  
...  
Keyword(s):  
South America ◽  
Tree Species ◽  
Large Scale ◽  
Environmental Filtering ◽  
Limiting Similarity ◽  
Phylogenetic Relatedness ◽  
Biogeographical Regions ◽  
Dependent Processes ◽  
Occurrence Of Species

AbstractSpecies co-occurrences in local communities can arise independent or dependent on species’ niches. However, the role of niche-dependent processes has not been thoroughly deciphered when generalized to biogeographical scales, probably due to combined shortcomings of data and methodology. Here, we explored the influence of environmental filtering and limiting similarity, as well as biogeographical processes that relate to the assembly of species’ communities and co-occurrences. We modelled jointly the occurrences and co-occurrences of 1016 tropical tree species with abundance data from inventories of 574 localities in eastern South America. We estimated species co-occurrences as raw and residual associations with models that excluded and included the environmental effects on the species’ co-occurrences, respectively. Raw associations indicate co-occurrence of species, whereas residual associations indicate co-occurrence of species after accounting for shared responses to environment. Generally, the influence of environmental filtering exceeded that of limiting similarity in shaping species’ co-occurrences. The number of raw associations was generally higher than that of the residual associations due to the shared responses of tree species to the environmental covariates. Contrary to what was expected from assuming limiting similarity, phylogenetic relatedness or functional similarity did not limit tree co-occurrences. The proportions of positive and negative residual associations varied greatly across the study area, and we found a significant tendency of some biogeographical regions having higher proportions of negative associations between them, suggesting that large-scale biogeographical processes limit the establishment of trees and consequently their co-occurrences.

scholarly journals Taxonomic assignment for large-scale metagenomic data on high-perfomance systems

2017 ◽  
Vol 33 (2) ◽  
pp. 119-130
Author(s):  
Vinh Van Le ◽  
Hoai Van Tran ◽  
Hieu Ngoc Duong ◽  
Giang Xuan Bui ◽  
Lang Van Tran
Keyword(s):  
High Performance Computing ◽  
Assignment Problem ◽  
High Performance ◽  
Large Scale ◽  
Computing System ◽  
Metagenomic Data ◽  
Taxonomic Assignment ◽  
High Performance Computing System ◽  
Powerful Approach ◽  
Performance Computing

Metagenomics is a powerful approach to study environment samples which do not require the isolation and cultivation of individual organisms. One of the essential tasks in a metagenomic project is to identify the origin of reads, referred to as taxonomic assignment. Due to the fact that each metagenomic project has to analyze large-scale datasets, the metatenomic assignment is very much computation intensive. This study proposes a parallel algorithm for the taxonomic assignment problem, called SeMetaPL, which aims to deal with the computational challenge. The proposed algorithm is evaluated with both simulated and real datasets on a high performance computing system. Experimental results demonstrate that the algorithm is able to achieve good performance and utilize resources of the system efficiently. The software implementing the algorithm and all test datasets can be downloaded at http://it.hcmute.edu.vn/bioinfo/metapro/SeMetaPL.html.

scholarly journals Comparative Cladistics: Fossils, Morphological Data Partitions and Lost Branches in the Fossil Tree of Life

2017 ◽  
Author(s):  
Ross Mounce
Keyword(s):  
Large Scale ◽  
Phylogenetic Signal ◽  
Scientific Progress ◽  
Molecular Data ◽  
Morphological Data ◽  
Data Sets ◽  
Phylogenetic Groups ◽  
Use Of Data ◽  
Wide Range ◽  
Cladistic Analyses

In this thesis I attempt to gather together a wide range of cladistic analyses of fossil and extant taxa representing a diverse array of phylogenetic groups. I use this data to quantitatively compare the effect of fossil taxa relative to extant taxa in terms of support for relationships, number of most parsimonious trees (MPTs) and leaf stability. In line with previous studies I find that the effects of fossil taxa are seldom different to extant taxa – although I highlight some interesting exceptions. I also use this data to compare the phylogenetic signal within vertebrate morphological data sets, by choosing to compare cranial data to postcranial data. Comparisons between molecular data and morphological data have been previously well explored, as have signals between different molecular loci. But comparative signal within morphological data sets is much less commonly characterized and certainly not across a wide array of clades. With this analysis I show that there are many studies in which the evidence provided by cranial data appears to be be significantly incongruent with the postcranial data – more than one would expect to see just by the effect of chance and noise alone. I devise and implement a modification to a rarely used measure of homoplasy that will hopefully encourage its wider usage. Previously it had some undesirable bias associated with the distribution of missing data in a dataset, but my modification controls for this. I also take an in-depth and extensive review of the ILD test, noting it is often misused or reported poorly, even in recent studies. Finally, in attempting to collect data and metadata on a large scale, I uncovered inefficiencies in the research publication system that obstruct re-use of data and scientific progress. I highlight the importance of replication and reproducibility – even simple reanalysis of high profile papers can turn up some very different results. Data is highly valuable and thus it must be retained and made available for further re-use to maximize the overall return on research investment.

scholarly journals Utilizing the VirIdAl Pipeline to Search for Viruses in the Metagenomic Data of Bat Samples

Viruses ◽  
2021 ◽  
Vol 13 (10) ◽  
pp. 2006
Author(s):  
Anna Y Budkina ◽  
Elena V Korneenko ◽  
Ivan A Kotov ◽  
Daniil A Kiselev ◽  
Ilya V Artyushin ◽  
...  
Keyword(s):  
Large Scale ◽  
High Throughput Sequencing ◽  
Metagenomic Data ◽  
Sequencing Data ◽  
Viral Pathogens ◽  
Genomic Databases ◽  
Bioinformatic Pipeline ◽  
Viral Genomes ◽  
Sequencing Technologies ◽  
Viral Screening

According to various estimates, only a small percentage of existing viruses have been discovered, naturally much less being represented in the genomic databases. High-throughput sequencing technologies develop rapidly, empowering large-scale screening of various biological samples for the presence of pathogen-associated nucleotide sequences, but many organisms are yet to be attributed specific loci for identification. This problem particularly impedes viral screening, due to vast heterogeneity in viral genomes. In this paper, we present a new bioinformatic pipeline, VirIdAl, for detecting and identifying viral pathogens in sequencing data. We also demonstrate the utility of the new software by applying it to viral screening of the feces of bats collected in the Moscow region, which revealed a significant variety of viruses associated with bats, insects, plants, and protozoa. The presence of alpha and beta coronavirus reads, including the MERS-like bat virus, deserves a special mention, as it once again indicates that bats are indeed reservoirs for many viral pathogens. In addition, it was shown that alignment-based methods were unable to identify the taxon for a large proportion of reads, and we additionally applied other approaches, showing that they can further reveal the presence of viral agents in sequencing data. However, the incompleteness of viral databases remains a significant problem in the studies of viral diversity, and therefore necessitates the use of combined approaches, including those based on machine learning methods.

A focus on pressure-driven membrane technology in olive mill wastewater reclamation: state of the art

2012 ◽  
Vol 66 (12) ◽  
pp. 2505-2516 ◽  
Author(s):  
J. M. Ochando-Pulido ◽  
A. Martinez-Ferez
Keyword(s):  
Olive Oil ◽  
Large Scale ◽  
Wastewater Treatment Plants ◽  
Domestic Wastewater ◽  
Olive Mill Wastewater ◽  
Operating Conditions ◽  
Added Value ◽  
Wastewater Reclamation ◽  
Starting Point ◽  
Olive Mill

Direct disposal of the heavily polluted effluent from olive oil industry (olive mill wastewater, OMW) to the environment or to domestic wastewater treatment plants is actually prohibited in most countries, and conventional treatments are ineffective. Membranes are currently one of the most versatile technologies for environmental quality control. Notwithstanding, studies on OMW reclamation by membranes are still scarce, and fouling inhibition and prediction to improve large-scale membrane performance still remain unresolved. Consequently, adequately targeted pretreatment for the specific binomium membrane-feed, as well as optimized operating conditions for the proper membranes, is today's challenge to ensure threshold flux values. Several membrane materials, configurations and pore sizes have been elucidated, and also different pretreatments including sedimentation, centrifugation, biosorption, sieving, filtration and microfiltration, various types of flocculation as well as advance oxidation processes have been applied so far. Recovery of potential-value compounds, such as a variety of polyphenols highlighting oleuropein and hydroxytyrosol, has been attempted too. All this research should constitute the starting point to proceed with OMW purification beyond recycling for irrigation or depuration for sewer discharge, with the aim of complying with standards to reuse the effluent in the olive oil production process, together with cost-effective recovery of added-value compounds.

scholarly journals Initial Mapping of the New York City Wastewater Virome

mSystems ◽  
2020 ◽  
Vol 5 (3) ◽  
Author(s):  
K. Gulino ◽  
J. Rahman ◽  
M. Badri ◽  
J. Morton ◽  
R. Bonneau ◽  
...  
Keyword(s):  
New York ◽  
New York City ◽  
York City ◽  
Wastewater Treatment Plants ◽  
Urban Environments ◽  
Metagenomic Data ◽  
Functional Importance ◽  
Wide Range ◽  
Viral Communities ◽  
Local Sampling

ABSTRACT Bacteriophages are abundant members of all microbiomes studied to date, influencing microbial communities through interactions with their bacterial hosts. Despite their functional importance and ubiquity, phages have been underexplored in urban environments compared to their bacterial counterparts. We profiled the viral communities in New York City (NYC) wastewater using metagenomic data collected in November 2014 from 14 wastewater treatment plants. We show that phages accounted for the largest viral component of the sewage samples and that specific virus communities were associated with local environmental conditions within boroughs. The vast majority of the virus sequences had no homology matches in public databases, forming an average of 1,700 unique virus clusters (putative genera). These new clusters contribute to elucidating the overwhelming proportion of data that frequently goes unidentified in viral metagenomic studies. We assigned potential hosts to these phages, which appear to infect a wide range of bacterial genera, often outside their presumed host. We determined that infection networks form a modular-nested pattern, indicating that phages include a range of host specificities, from generalists to specialists, with most interactions organized into distinct groups. We identified genes in viral contigs involved in carbon and sulfur cycling, suggesting functional importance of viruses in circulating pathways and gene functions in the wastewater environment. In addition, we identified virophage genes as well as a nearly complete novel virophage genome. These findings provide an understanding of phage abundance and diversity in NYC wastewater, previously uncharacterized, and further examine geographic patterns of phage-host association in urban environments. IMPORTANCE Wastewater is a rich source of microbial life and contains bacteria, viruses, and other microbes found in human waste as well as environmental runoff sources. As part of an effort to characterize the New York City wastewater metagenome, we profiled the viral community of sewage samples across all five boroughs of NYC and found that local sampling sites have unique sets of viruses. We focused on bacteriophages, or viruses of bacteria, to understand how they may influence the microbial ecology of this system. We identified several new clusters of phages and successfully associated them with bacterial hosts, providing insight into virus-host interactions in urban wastewater. This study provides a first look into the viral communities present across the wastewater system in NYC and points to their functional importance in this environment.

scholarly journals The Distribution of Tryptophan-Dependent Indole-3-Acetic Acid Synthesis Pathways in Bacteria Unraveled by Large-Scale Genomic Analysis

Molecules ◽  
2019 ◽  
Vol 24 (7) ◽  
pp. 1411 ◽  
Author(s):  
Pengfan Zhang ◽  
Tao Jin ◽  
Sunil Kumar Sahu ◽  
Jin Xu ◽  
Qiong Shi ◽  
...  
Keyword(s):  
Acetic Acid ◽  
Large Scale ◽  
Growth Promotion ◽  
Plant Root ◽  
Genomic Analysis ◽  
Acid Synthesis ◽  
Metagenomic Data ◽  
Bacterial Genomes ◽  
Bacterial Phyla ◽  
Indole 3 Acetic Acid

Bacterial indole-3-acetic acid (IAA), an effector molecule in microbial physiology, plays an important role in plant growth-promotion. Here, we comprehensively analyzed about 7282 prokaryotic genomes representing diverse bacterial phyla, combined with root-associated metagenomic data to unravel the distribution of tryptophan-dependent IAA synthesis pathways and to quantify the IAA synthesis-related genes in the plant root environments. We found that 82.2% of the analyzed bacterial genomes were potentially capable of synthesizing IAA from tryptophan (Trp) or intermediates. Interestingly, several phylogenetically diverse bacteria showed a preferential tendency to utilize different pathways and tryptamine and indole-3-pyruvate pathways are most prevalent in bacteria. About 45.3% of the studied genomes displayed multiple coexisting pathways, constituting complex IAA synthesis systems. Furthermore, root-associated metagenomic analyses revealed that rhizobacteria mainly synthesize IAA via indole-3-acetamide (IAM) and tryptamine (TMP) pathways and might possess stronger IAA synthesis abilities than bacteria colonizing other environments. The obtained results refurbished our understanding of bacterial IAA synthesis pathways and provided a faster and less labor-intensive alternative to physiological screening based on genome collections. The better understanding of IAA synthesis among bacterial communities could maximize the utilization of bacterial IAA to augment the crop growth and physiological function.

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