Determination of lab-scale biomethane potential of wheat straw pellets and their influence on anaerobic digestion

Laboratory scale degradation of wheat straw pellets as an additional substrate for methane production was monitored as an example of controlled usage of unconventional substrates. In the laboratory biomethane potential of input feedstock from biogas plant (BGP) Organica Nova to which pellets were added in different proportions was determined. Organic loading (volatile solids, VS) was 5 g VS/L in all cases. Measurements were carried out by AMPTS I (Bioprocess Control, Sweden). Amount of produced methane was monitored and environmental conditions such as pH, TS, VS and temperature were measured.\ud The coefficient of hydrolysis of straw pellets and mixture of straw pellets and substrate from BGP Organica Nova in anaerobic digestion process was determined. Mixture where straw pellets presented 10 % organic loading rate of substrate added to the reactor achieved the biomethane potential of 352 mL CH4/g VS. In the case of using only the substrate from the BPE Organica Nova the highest methane yield of 438 mL CH4/g VS was achieved.\u

Determination of lab-scale biomethane potential of wheat straw pellets and their influence on anaerobic digestion

Laboratory scale degradation of wheat straw pellets as an additional substrate for methane production was\ud monitored as an example of controlled usage of unconventional substrates. In the laboratory biomethane\ud potential of input feedstock from biogas plant (BGP) Organica Nova to which pellets were added in different\ud proportions was determined. Organic loading (volatile solids, VS) was 5 g VS/L in all cases. Measurements\ud were carried out by AMPTS I (Bioprocess Control, Sweden). Amount of produced methane was monitored\ud and environmental conditions such as pH, TS, VS and temperature were measured.\ud The coefficient of hydrolysis of straw pellets and mixture of straw pellets and substrate from BGP Organica\ud Nova in anaerobic digestion process was determined. Mixture where straw pellets presented 10 % organic loading rate of substrate added to the reactor achieved the biomethane potential of 352 mL CH4/g VS. In the\ud case of using only the substrate from the BPE Organica Nova the highest methane yield of 438 mL CH4/g\ud VS was achieved

Overview of data preprocessing for machine learning applications in human microbiome research

Although metagenomic sequencing is now the preferred technique to study microbiome-host interactions, analyzing and interpreting microbiome sequencing data presents challenges primarily attributed to the statistical specificities of the data (e.g., sparse, over-dispersed, compositional, inter-variable dependency). This mini review explores preprocessing and transformation methods applied in recent human microbiome studies to address microbiome data analysis challenges. Our results indicate a limited adoption of transformation methods targeting the statistical characteristics of microbiome sequencing data. Instead, there is a prevalent usage of relative and normalization-based transformations that do not specifically account for the specific attributes of microbiome data. The information on preprocessing and transformations applied to the data before analysis was incomplete or missing in many publications, leading to reproducibility concerns, comparability issues, and questionable results. We hope this mini review will provide researchers and newcomers to the field of human microbiome research with an up-to-date point of reference for various data transformation tools and assist them in choosing the most suitable transformation method based on their research questions, objectives, and data characteristics

Broad diversity of bacteria degrading 17ß-estradiol-3-sulfate isolated from river sediment and biofilm at a wastewater treatment plant discharge

Erworben im Rahmen der Schweizer Nationallizenzen (http://www.nationallizenzen.ch)Conjugated estrogens, such as 17β-estradiol-3-sulfate (E2-3S), can be released into aquatic environments through wastewater treatment plants (WWTP). There, they are microbiologically degraded into free estrogens, which can have harmful effects on aquatic wildlife. Here, the degradation of E2-3S in environmental samples taken upstream, downstream and at the effluent of a WWTP was assessed. Sediment and biofilm samples were enriched for E2-3S-degrading microorganisms, yielding a broad diversity of bacterial isolates, including known and novel degraders of estrogens. Since E2-3S-degrading bacteria were also isolated in the sample upstream of the WWTP, the WWTP does not influence the ability of the microbial community to degrade E2-3S

How Can We Advance Integrative Biology Research in Animal Science in 21st Century?:Experience at University of Ljubljana from 2002 to 2022

In this perspective analysis, we strive to answer the following question: how can we advance integrative biology research in the 21st century with lessons from animal science? At the University of Ljubljana, Biotechnical Faculty, Department of Animal Science, we share here our three lessons learned in the two decades from 2002 to 2022 that we believe could inform integrative biology, systems science, and animal science scholarship in other countries and geographies. Cultivating multiomics knowledge through a conceptual lens of integrative biology is crucial for life sciences research that can stand the test of diverse biological, clinical, and ecological contexts. Moreover, in an era of the current COVID-19 pandemic, animal nutrition and animal science, and the study of their interactions with human health (and vice versa) through integrative biology approaches hold enormous prospects and significance for systems medicine and ecosystem health

Antibiotic-resistant soil bacteria in high-altitude (5000-6000 m) soils of the Himalaya

In this study, low-carbon soils collected from an altitude transect from 5000 m to 6000 m were adopted as a simple model system with lower interaction complexity. This could help disentangle the basic environmental factors shaping the abundance and distribution of expressed resistance traits in culturable portion of fast growing heterotrophic strains. Improved plate counts were performed at 4 °C using 0.01 diluted nutrient broth supplemented with cold soil extract as a general media and additionally supplemented with antibiotics Ampicillin, Erzthromycin, Kanamycin and Tetracyclin. A number of colonies (500) isolated from six locations were also tested separately for their antibiotic resistance. The results show that these high-altitude cold soils contained bacterial populations culturable at 4 °C in the range of 106 cells / g that were resistant to the four antibiotics and their various combinations tested in this study. The highest prevalence of resistance was observed in vegetated soils, whereas almost two orders of magnitude lower abundance of resistant cells was cultured from barren soils. Redundancy analysis showed that vegetation, soil carbon and pH were successful in explaining the interaction between environmental parameters and various culturable fractions of cold soil bacteria used in this study.V študiji sem uporabil vzorce tal z nizko vsebnostjo organskega ogljika iz višinskega transekta 5000 m- 6000 m kot poenostavljen modelni sistem z nizko kompleksnostjo interakcij. Ta bi lahko pomagal razumeti osnovne okoljske dejavnike, ki uravnavajo porazdelitev in obseg izraženih rezistenčnih lastnosti gojljivega dela hitro rastočih heterotrofnih sevov. Izboljšano štetje na ploščah sem izvedel pri 4 °C na 0,01 koncentriranem hranilnem bujonu, dopolnjenim s hladnim ekstraktom tal, kot splošnim gojiščem, ki sem ga dopolnil z posameznimi antibiotiki (ampicilin, eritromicin, kanamicin in tetraciklin). Večje število izolatov (500) iz šestih lokacij sem prav tako testiral ločeno na njihovo odpornost na antibiotike. Ugotavljal sem tudi povezavo med okoljskimi dejavniki ter porazdelitvijo odpornih sevov in splošnega gojljivega delea talnih bakterij. Rezultati kažejo, da visokogorska hladna tla vsebujejo pri nizkih temperaturah gojljive bakterijske populacije (106 / g), ki so odporni na posamezne antibiotike in razne njihove kombinacije, uporabljene v tej študiji. Poraščena tla imajo največji dele odpornih bakterij, skoraj dva reda manjši pa je prisoten v golih tleh. Statistična analiza je pokazala, da vegetacija, organski ogljik ter pH uspešno razložijo interakcijo med okoljskimi dejavniki in posameznimi gojenimi deleži bakterij, izoliranih iz hladnih tal

Prvo destletje restrikcijskega polimorfizma dolžine končnih fragmentov (T-RFLP) v mikrobni ekologiji

Terminal restriction fragment length polymorphism (T-RFLP) was introduced to environmental microbiology only a decade ago but it soon became a molecular tool of choice, due to its high throughput and phylogenetic resolution. Fierce discussions accompanied the new method leading to sophistication of the data preparation, acquisition, manipulation and standardization of analysis. Consequently, numerous approaches were proposed at various steps and also criticized. As a result, a combination of variable percentage threshold and Bray-Curtis index used in non-metric multidimensional scaling are now being accepted. Their combination offers a balance between noise elimination and information retention yielding a powerful and yet easily interpreted method toexamine community patterns based on T-RFLP data. Its current state of the art and future developments highlight the potential of the method in the field of microbial ecology. However, a more standardized approach and a higher level of control at all stages of T-RFLP fingerprinting are needed.Proučevanje restrikcijskega polimorfizma dolžine končnih fragmentov (T-RFLP) tarčnih genov se na področju mikrobne ekologije pričelo šele pred desetletjem. Metoda je hitro postala zelo priljubljena zaradi svoje filogenetske ločljivosti in enostavne analize velikega števila vzorcev. Razvoj priprave vzorcev, zajemanja podatkov, obdelave in standardizacije metod analize so v veliki meri obkrožale silovite razprave. Raziskovalci so tako na vsaki stopnji kritično preizkusili veliko število različnih pristopov. Danes kombinacija tehnik, kot so prag variabilnih deležev, koeficient Bray-Curtis v ne-merskem večdimenzionalnem umerjanju predstavlja ravnotežje med odstranjevanjem suma in zadrževanjem informacij. Tako je nastalo zelo uporabno orodje z relativno enostavno interpretacijo za proučevanje tipizacijskih profilov T-RFLP mikrobnih združb. Njegova trenutna stopnja dovršenosti in predvidene razvojne izpopolnitve v prihodnosti kažejo na velik potencial tega orodja na področju mikrobne ekologije. Hkrati pa bo potrebno uveljaviti tudi bolj standardizirane in bolje kontrolirane izvedbe posameznih stopenj tipizacije mikrobnih združb s T-RFLP

Computational framework for high-quality production and large-scale evolutionary analysis of metagenome assembled genomes

Microbial species play important roles in different environments and the production of high-quality genomes from metagenome data sets represents a major obstacle to understanding their ecological and evolutionary dynamics. Metagenome-Assembled Genomes Orchestra (MAGO) is a computational framework that integrates and simplifies metagenome assembly, binning, bin improvement, bin quality (completeness and contamination), bin annotation, and evolutionary placement of bins via detailed maximum-likelihood phylogeny based on multiple marker genes using different amino acid substitution models, next to average nucleotide identity analysis of genomes for delineation of species boundaries and operational taxonomic units. MAGO offers streamlined execution of the entire metagenomics pipeline, error checking, computational resource distribution and compatibility of data formats, governed by usertailored pipeline processing. MAGO is an open-source-software package released in three different ways, as a singularity image and a Docker container for HPC purposes as well as for running MAGO on a commodity hardware, and a virtual machine for gaining a full access to MAGO underlying structure and source code. MAGO is open to suggestions for extensions and is amenable for use in both research and teaching of genomics and molecular evolution of genomes assembled from small single-cell projects or large-scale and complex environmental metagenomes

Efficient coding of DNA

V zadnjem obdobju smo priča znatnemu naraščanju uporabe mikroračunalnikov pri raziskavah in analizah zaporedij DNA. Molekule DNA so računalnikom najpogosteje predstavljene v obliki zapisov v formatu FASTA , ki kodirajo sekvence DNA v obliki ASCII niza štirih nukleotidnih oznak A, G, C in T, katerim se po potrebi pridružijo še degenerativne kode in znak za presledek, ko gre za množice med seboj poravnanih zaporedij DNA. Zapis FASTA je dojemljiv za biologa in enostaven za programerja, ki razvija računalniški program, saj si pri razvoju lahko pomaga z bogatim naborom obstoječih knjinic za delo z znakovnimi polji. Kljub omenjenim prednostim ima zapis FASTA določene slabosti, kot je manj učinkovito iskanje zaporedij nukleotidov, še posebej ob prisotnosti degenerativnih kod. Druga slabost izvira iz dejstva, da vsak posamezni znak FASTA za presledek zasede po en zlog računalniškega pomnilnika,kar je ob prisotnosti velikega števila presledkov neučinkovito in tudi dodatno manjša hitrost iskanja nukleotidnih zaporedij. Zaradi omenjenih slabosti predstavljamo alternativni zapis zaporedij DNA, ki omogoča hitrejše iskanje nukleotidnih zaporedij in učinkovitejše shranjevanje informacij o poravnavi, kar vodi v hitrejše delovanje programov in odpira monost shranjevanja večjega števila zapisov DNA v delovni pomnilnik računalnika.Microcomputers have become ubiquitous tools for DNA research and analysis. Before DNA sequences can be fed into computer programs they need to be suitably coded, which is usually done in a widely accepted FASTA format. According to this scheme, DNA sequence is represented as an ASCII string of four nucleotide characters A, G, C and T, possibly extended with additional codes for representation of degenerated sites, and a character code for FASTA blanks when dealing with aligned DNA sequences. FASTA representation is intuitive for biologists and it eases development of programs since developer scan utilize a myriad of available libraries for working with ASCII strings. Despite the mentioned advantages, FASTA format possesses certain drawbacks like inefficient searching for substrings, especially in the presence of degenerative codes. The second disadvantage is inefficient storage of FASTA blank characters, since each such character occupies one byte of memory. Substring searching speed is also negatively affected in the case of excessive number of blanks. Due to the stated drawbacks, we propose an alternative coding of DNA sequences, which enables faster searching of substrings and efficient storage of FASTA blanks, with the result that a greater set of DNA sequences can be held in working memory of a computer and processed faster

New primer combinations with comparable melting temperatures detecting highest numbers of nosZ sequences from sequence databases

We explored existing primer sequences targeting nitrous oxide reductase (nosZ) gene in order to explore their capability to recognize variant nosZ sequences. Published nosZ sequences longer than 380 AA residues were obtained from FunctionalGene Database /Repository (http://flyingcloud.cme.msu.edu/fungene/) and used for explorations with PrimerChart program. The numbers of sequences recovered using all possible forward and reverse primer combinations were determined and the stringency of primer site recognition was further varied by allowing 1, 2, or 3 primer mismatches to DNA binding site. We identified novel primer combinations resulting in satisfactory amplicon length (> 500 bp) and increased sequence recognition capabilities at comparable forward and reverse primer melting temperatures. Overall, this study indicates that current state of the art molecular methods can be and should frequently be further refined by the use of targeted bioinformatic approaches.V tej študiji sva raziskala obstoječe sekvence začetnih oligonukleotidov, s katerimi se pomnožujejo fragmenti gena za reduktazo N2O (nosZ), da bi proučila njihovo zmožnost prepoznavanja variant sekvenc nosZ. Objavljene sekvence gena nosZ daljše od 380 aminokislninskih ostankov sva pridobila od FunctionalGene Database /Repository (http://flyingcloud.cme.msu.edu/fungene/) in jih analizirala s programom PrimerChart. Raziskala sva število, ki ga prepoznajo posamične mone kombinacije yačetnih oligonukleotidov. V nadaljevanju sva spreminjala natančnost prileganja začetnih oligonukleotidov na tarčno DNK tako, da sva dovolila 1, 2, or 3 napačna parjenja med začetnim oligonukleotidom in DNK. Tako sva identificirala nove kombinacije začetnih oligonukleotidov, ki ustvarijo ustrezno dolge fragmente (> 500 bp), s povišano sposobnostjo prepoznavanja sekvenc pri primerljivi temperaturi taljenja začetnih oligonukleotidov. Prav tako so se nakazale nove možnosti za izboljšanje začetnih oligonukleotidov z vnosom novih degeneriranih mest. Ta študija nakazuje, da je novejše molekularne metode možno in tudi potrebno pogosto nadgrajevati s ciljanimi bioinformatskimi pristopi