Higher Relative Abundance Research Articles

Bacterial profile of pork from production to retail based on high-throughput sequencing

Pork is a common vehicle for foodborne pathogens, including Salmonella spp. and Yersinia enterocolitica. Cross-contamination can occur at any stage of the pork production chain, from farm to market. In the present study, high-throughput sequencing was used to characterize bacterial profiles and track their changes along the whole supply chain. Tracked meat samples (pig on the farm, carcass in the slaughterhouse, unprocessed carcass and processed meat in the processing plant, and fresh pork at the local retail stores) and their associated environmental samples (e.g., water, floor, feed, feces, and workers' gloves) were collected from sequential stages (n = 96) and subjected to 16S rRNA metataxonomic analyses. At the farm, a total of 652 genera and 146 exclusive genera were identified in animal and environmental samples (pig, drain, floor, fan, and feces). Based on beta diversity analysis, it was demonstrated that the microbial composition of animal samples collected at the same processing step is similar to that of environmental samples (e.g., drain, fan, feces, feed, floor, gloves, knives, tables, and water). All animal and environmental samples from the slaughterhouse were dominated by Acinetobacter (55.37 %). At the processing plant, belly meat and neck meat samples were dominated by Psychrobacter (55.49 %). At the retail level, key bacterial players, which are potential problematic bacteria and important members with a high relative abundance in the samples, included Acinetobacter (8.13 %), Pseudomonas (6.27 %), and Staphylococcus (2.13 %). In addition, the number of confirmed genera varied by more than twice that identified in the processing plant. Source tracking was performed to identify bacterial contamination routes in pork processing. Animal samples, including the processing plant's carcass, the pig from the farm, and the unwashed carcass from the slaughterhouse (77.45 %), along with the processing plant's gloves (5.71 %), were the primary bacterial sources in the final product. The present study provides in-depth knowledge about the bacterial players and contamination points within the pork production chain. Effective control measures are needed to control pathogens and major pollutants at each stage of pork production to improve food safety.

Effect of castration timing and weaning strategy on the taxonomic and functional profile of ruminal bacteria and archaea of beef calves

BackgroundBeef cattle experience several management challenges across their lifecycle. Castration and weaning, two major interventions in the early life of beef cattle, can have a substantial impact on animal performance. Despite the key role of the rumen microbiome on productive traits of beef cattle, the effect of castration timing and weaning strategy on this microbial community has not been formally described. We assessed the effect of four castration time windows (at birth, turnout, pre-weaning and weaning) and two weaning strategies (fence-line and truck transportation) on the rumen microbiome in a randomized controlled study with 32 male calves across 3 collection days (i.e., time points). Ruminal fluid samples were submitted to shotgun metagenomic sequencing and changes in the taxonomic (microbiota) and functional profile (metagenome) of the rumen microbiome were described.ResultsUsing a comprehensive yet stringent taxonomic classification approach, we identified 10,238 unique taxa classified under 40 bacterial and 7 archaeal phyla across all samples. Castration timing had a limited long-term impact on the rumen microbiota and was not associated with changes in alpha and beta diversity. The interaction of collection day and weaning strategy was associated with changes in the rumen microbiota, which experienced a significant decrease in alpha diversity and shifts in beta diversity within 48 h post-weaning, especially in calves abruptly weaned by truck transportation. Calves weaned using a fence-line weaning strategy had lower relative abundance of Bacteroides, Lachnospira, Fibrobacter and Ruminococcus genera compared to calves weaned by truck transportation. Some genes involved in the hydrogenotrophic methanogenesis pathway (fwdB and fwdF) had higher relative abundance in fence-line-weaned calves post-weaning. The antimicrobial resistance gene tetW consistently represented more than 50% of the resistome across time, weaning and castration groups, without significant changes in relative abundance.ConclusionsWithin the context of this study, castration timing had limited long-term effects on the rumen microbiota, while weaning strategy had short-term effects on the rumen microbiota and methane-associated metagenome, but not on the rumen resistome.

Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits

The composition and function of the intestinal microbiota are major determinants of human health and are strongly influenced by diet, antibiotic treatment, lifestyle and geography. Nevertheless, we currently have only little data on microbiomes of non-westernized communities. We assess the stool microbiota composition in 59 children aged 2–5 years from the Adadle district of Ethiopia, Somali Regional State. Here, milk and starch-rich food are predominant components of the local diet, where the inhabitants live a remote, traditional agropastoral lifestyle. Microbiota composition, function and the resistome were characterized by both 16S rRNA gene amplicon and shotgun metagenomic sequencing and compared to 1471 publicly available datasets from children living in traditional, transitional, and industrial communities with different subsistence strategies. Samples from the Adadle district are low in Bacteroidaceae, and Prevotellaceae, the main bacterial representatives in the feces of children living in industrialized and non-industrialized communities, respectively. In contrast, they had a higher relative abundance in Streptococcaceae, Bifidobacteriaceae and Erysipelatoclostridiaceae. Further, genes involved in degradation pathways of lactose, d-galactose and simple carbohydrates were enriched. Overall, our study revealed a unique composition of the fecal microbiota of these agropastoral children, highlighting the need to further characterize the fecal bacterial composition of human populations living different lifestyles.

Bacterial community and sensory quality from coffee are affected along fermentation under carbonic maceration

The diversity and activity of the indigenous microorganisms in coffee are essential for obtaining safe and good-quality coffee. The use of fermentation under carbonic maceration in coffee fruits showed a positive correlation between the bacterial community and sensory score. Thus, the objective of this study was to evaluate the bacterial diversity in coffee cherries during fermentation under carbonic maceration and their correlations with coffee-quality. Next-generation sequencing and Specialty Coffee Association protocol were used in this study. Predominance of Leuconostoc sp. and Lactobacillus sp. during fermentation was observed. Leuconostoc sp. had higher relative abundance in the initial phase of fermentation and at 18 and 28 °C than Lactobacillus sp. Furthermore, the greatest microbial diversity occurred at 38 °C and after 72 h. At this temperature, the relative abundance of Lactobacillus correlated positively with sensorial score. Thus, an increase in temperature and fermentation time favors Lactobacillus spp and coffee sensory quality.

Composition and diversity of the gut microbiota across different life stages of American cockroach (Periplaneta americana).

Periplaneta americana, one of the most widely distributed insects all over the world, can survive and reproduce in harsh environment which may be closely related to the critical roles of intestinal microorganisms in its multiple physiological functions. However, the composition and structure of gut microbiota throughout different life stages and its effects on the strong resilient and environmental adaptability of P. americana remain unclear. In this study, the gut microbiota across life stages including ootheca (embryos), nymph and adult of P. americana were investigated by 16S rRNA high-throughput sequencing. Multivariate statistical analysis showed the richness and diversity of bacterial communities were significantly different among ootheca, nymph and adult stage of P. americana. Taxonomic analysis showed Blattabacterium was the dominant genus in bacterial community of ootheca while the nutrient absorption-related genera including Christensenellaceae and Ruminococcaceae showed high relative abundance in nymph samples. Moreover, functional prediction analysis showed the metabolic categories in ootheca might have more influence on the basic life activities of the host than improved production and viability, while it was more associated to the society activities, reproduction and development of host in nymph and adult. It was suggested that the gut microbiota in each life stage might meet the requirements for environmental adaptability and survival of P. americana via transforming the composition and structure with specific metabolic capabilities. Overall, these results provided a novel sight to better understand the strong vitality and adaptability throughout life stages of P. americana.

Microbial spatiotemporal succession and metabolic difference in multidimensional pit mud used for the production of Luzhou-flavor baijiu

Pit mud (PM) prokaryotic community is essential for the solid-fermentation of Luzhou-flavor baijiu. In this study, the multidimensional (four vertical positions) microbial communities of different PMs were investigated. Microbial communities were significantly different in multidimensional PMs (p = 0.001). Horizontally speaking, the relative abundance of Longilinea at the position 1 (bottom of the cellar) was highest in 30-year PMs (16.19%) and decreased gradually in 100- (11.95%) and 300-year (0.27%) PMs. Methanobrevibacter had the highest relative abundance at the position 3 (up the huangshui fluid) in 100-year PMs (18.98%), and decreased in 300-year PMs (8.73%), at the position 4 (top site of the cellar), Clostridium had the highest abundance in 100-year PMs (8.24%). Vertically speaking, Petrimonas had the highest abundance (17.4%) at the position 3 in 100-year PMs, while for the 300-year PMs, Lactobacillus and Caproiciproducens had the highest abundance at the position 1. RDA analysis indicated that lactic, caproic, butyric, and acetic acids were the four key physicochemical factors. Amino acids, peptides, fatty acids, and conjugates were the main metabolites of PMs, and S-Acetyldihydrolipoamide-E, succinic acid, aspartic acid, asparagine and valine were key differential metabolites. Based on OPLS-DA analysis, 20 differential flavor compounds were identified, mainly including esters such as hexanoic acid methyl ester, ethyl acetate, hexanoic acid ethyl ester, butanoic acid hexyl ester and acids such as hexanoic acid, butanoic acid and heptanoic acid. Moreover, hexanoic, octanoic acid and their corresponding esters were concentrated on 300-year PMs. This study provides theoretical support for improving the quality of PM.

Effect of dietary phytase on water and fecal prokaryotic and eukaryotic microbiomes in a hybrid tilapia (Oreochromis aureus x O. niloticus) mixotrophic biofloc production system

In this study we evaluated feed and temporal effects on prokaryotic (16S) and eukaryotic (18S) microbiome dynamics in an outdoor mixotrophic biofloc system used to grow hybrid tilapia (Oreochromis aureus x O. niloticus) to market size. The dicalcium phosphate -free practical feed treated with 6-phytase (3000 FTU/kg; P-Free+Phytase) and positive (Control) and negative (P-Free) control practical feeds used were formulated to contain 27.7% digestible protein and 4% lipid. Sex reversed, all-male hybrid tilapia (28.9 g/fish) were stocked (29 fish/m3) in 9 outdoor rectangular tanks (16.6 m3) and grown for 154 days. The Control feed was fed to all fish during the 14-day acclimation period after which each test feed was fed to fish in three tanks/feed. Biofloc water and fecal samples were collected from all tanks at time 0 (T0, study day 15) and T7, T70, and T140; prokaryotic and eukaryotic abundance and diversity were assessed using high-throughput amplicon sequencing of the 16S and 18S rRNA genes, respectively. Fecal 16S microbiome in all treatments was dominated by Fusobacteria (namely Cetobacterium) with minority representation by Proteobacteria, Firmicutes, Bacteroidetes, and Planctomycetes. Opisthokonts (namely Capsaspora) were the dominant eukaryote detected overall in all fecal samples. Fecal 16S and 18S relative abundances varied significantly with time. Relative abundance of fecal 16S differed significantly between Control and P-Free+Phytase feed treatments only at T140 (harvest). Fecal 18S relative abundance differences among feed treatments were detected only at T0 and T7 and only at the supergroup taxonomic level. Prokaryotic communities in biofloc water among feed treatments and across times were highly diverse and dominated by Proteobacteria, Bacteroidetes, Fusobacteria, Chloroflexi, Planctomycetes, and Actinobacteria. High relative abundances of Capsaspora across time characterized eukaryotic communities. Relative abundances of 16S and 18S taxa in water varied significantly over time. Control and P-Free feed 16S relative abundances in water differed significantly at T0 and T7. Time was the factor that explained most of the variation observed for 16S and 18S beta diversity. Overall, results of the present experiment suggest minimal influence of phytase-treated or dicalcium phosphate-free feeds on hybrid tilapia 16S and 18S water and fecal microbiomes throughout the experiment, particularly because the base feed formulation was the same for all treatments. During this experiment and at harvest tilapia in all treatments appeared healthy and robust, and no known pathogenic bacteria or eukaryotes were detected in any sample, suggesting the observed microbiomes may represent system-specific “healthy” core microbiomes.

Gut Microbial Diversity Analysis of Different Native Chickens and Screening of Chicken-Derived Probiotics

The gut microbiota plays a critical role in the growth, development, nutritional digestion, and overall health of chickens. Furthermore, certain probiotics isolated from poultry intestines have demonstrated the potential to enhance immune function and production performance in chickens. To investigate the differences in gut microbiota among chickens from various geographical environments and different breeds of broiler and laying hens, we conducted 16S rRNA sequencing on the fecal microbiota of 140 Chinese native chickens and ten Roman layers. In addition, we isolated and screened the potential probiotics to examine their biological characteristics, genome profiles, and functionality in animals. Our findings revealed the significant variations in gut microbiota composition and structure between Tibetan chickens (ZJ), which reside in high-altitude regions, and Meihua chickens (MH) and Xuhai chickens (XH), which inhabit low-altitude regions. Specifically, Cupriavidus and Candidatus_Bacilloplasma were identified as unique microbial communities in high and low altitudes, respectively. Notably, among regions with similar altitudes, Luning chickens (LN) exhibited the lowest α diversity, accompanied by a remarkably high relative abundance of Firmicutes and Lactobacillus. Conversely, Wugu chickens (WGs) and Yaoshan chickens (YSs) displayed similar gut microbiota profiles. Furthermore, distinctive gut microbiota patterns were observed between the different breeds of broilers and laying hens. Commercial Roman layers (LMs) exhibited significantly lower alpha diversity compared to native chickens, and broilers and laying hens predominantly harbored Firmicutes, Bacteroidota, and Proteobacteria. Of particular interest, the probiotics Lactobacillus agilis MH1 and Lactobacillus salivarius ZJ1, derived from chicken feces, exhibited favorable genomic profiles, and demonstrated anti-colitis effects and immunomodulatory functions. These findings provide a crucial theoretical foundation for native chicken research and offer insights for the future development and formulation of chicken-derived probiotics.

Effect of antibiotics addition on nutrient removal stability and microbial community change of the solar-powered oxidation ditch-membrane bioreactor in treating building wastewater

The solar-powered oxidation ditch-membrane bioreactors (SOD-MBR) system was developed and operated with long solid retention times (SRTs) of 80 and 160 days. The aim was to investigate the effects of using a long SRT and antibiotics in building wastewater on the stability of nutrient removal, as well as membrane fouling. An increase in the SRT from 80 days to 160 days did not significantly affect the performance of the SOD-MBR system. Ciprofloxacin and Sulfamethoxazole removal efficiencies were 94.47 ± 1.54% and 87.54 ± 24.7%. However, the presence of antibiotics resulted in lower removal efficiencies for NH4+-nitrogen and phosphorus and stimulated the production of extracellular polymeric substances (EPS), particularly proteins in L-EPS and T-EPS of the foulant. FTIR and FEEM analysis revealed that the microbial sludge primarily consisted of proteins, carbohydrates, and lipids. Furthermore, the relative abundance analysis of microbial communities identified bacteria associated with nitrogen removal in the SOD-MBR system, including Anammox, AOB (ammonia oxidizing bacteria), DNB (denitrifying bacteria), and NOB (nitrite oxidizing bacteria), with a total of 25 genera. The majority of these bacteria were stimulated by the presence of antibiotics, resulting in higher relative abundance. Finally, the SOD-MBR system achieved energy savings of 97.38% by utilizing photovoltaic (PV) technology.

Rare resistome rather than core resistome exhibited higher diversity and risk along the Yangtze River

As important freshwater ecosystems, the occurrence and distribution of antibiotic resistance genes (ARGs) in rivers are relevant to public health. However, studies investigating ARGs of different environmental media in river ecosystems are limited. In this study, we analyzed the ARGs of microbes in free-living setting, particle-associated setting, sediment and bank soil of the Yangtze River using metagenomics. Twenty-six ARGs were found in all samples regardless of media (core resistome) with a diversity of 8.6 %-34.7 %, accounting for 22.7 %-89.2 % of the relative abundance of the overall ARGs. The core resistome of the Yangtze River was dominated by multidrug resistance genes consisting mainly of efflux pumps and bacitracin resistance genes. The rare resistome was dominated by multidrug, sulfonamide, and aminoglycoside resistance genes. The core resistome was more prevalent in chromosomes, implying that these ARGs with low diversity and high relative abundance may be intrinsic to microbes in the Yangtze River. The rare resistome was more prevalent in plasmids, suggesting these ARGs with high diversity and low relative abundance were acquired under environmental stresses and had transfer potential. Additionally, we found that core and rare resistome were mainly carried by specific bacteria. Noteworthily, twenty-two ARGs of high clinical concern were identified in rare resistome, especially aac(6′)-I, sul1, and tetM, which were plasmid-borne and hosted by clinically relevant pathogens. Both core and rare resistome hosts showed the highest niche breadths in particle-associated setting compared to other media, and particle-associated setting could provide more stable and ideal conditions for resistome hosts to survive. This study elucidated the genetic locations of ARGs and the community assembly mechanisms of ARG hosts in freshwater environments.

Side effects of the addition of an adsorbent for the nitrification performance of a microbiome in the treatment of an antibiotic mixture

This work determined the effect of biochar (BC) as an adsorbent on the nitrifying microbiome in regulating the removal, transformation, fate, toxicity, and potential environmental consequences of an antibiotic mixture containing oxytetracycline (OTC) and sulfamethoxazole (SMX). Despite the beneficial role of BC as reported in the literature, the present study revealed side effects for the nitrifying microbiome and its functioning arising from the presence of BC. Long-term monitoring revealed severe disruption to nitratation via the inhibition of both nitrite oxidizers (e.g., Nitrospira defluvii) and potential comammox species (e.g., Ca. Nitrospira nitrificans). Byproducts (BPs) more toxic than the parent compounds were found to persist at a high relative abundance, particularly in the presence of BC. Quantitative structure–activity relationship modeling determined that the physicochemical properties of the toxic BPs significantly differed from those of OTC and SMX. The results suggested that the BPs tended to mobilize and accumulate on the surface of the solids in the system (i.e., the BC and biofilm), disrupting the nitrifiers growing at the interface. Collectively, this study provides novel insights, demonstrating that the addition of adsorbents to biological systems may not necessarily be beneficial; rather, they may generate side effects for specific bacteria that have important ecosystem functions.

The implication of seaweed farming on seagrass and seagrass-associated communities in Pemba, Zanzibar

The effect of seaweed farming on seagrass and its associated community was investigated on Pemba Island. Seagrass biometrics and macrofauna diversity were evaluated in seaweed plots (SP), seagrass meadows, Thalassia hemprichii (Th), mixed seaweed plots and seagrass (ThSP+) and bare sand (BS). Results revealed significantly higher (p = 0.001) seagrass biometric characteristics in Th compared to ThSP+ . Kruskal-Wallis test (χ2 _54.24 p = 0.001) showed a significant difference between habitats, with higher relative abundance in Th. Macrofauna diversity was significantly higher (p = 0.001) in Th compared to other habitats. Shannon-Weiner and Simpson's indexes ranked all habitats as the most diverse except SP and BS. The findings showed the negative effects of seaweed farming on seagrass and its associated community. This could be due to frequent trampling and boat mooring. Although seaweed farming is an economic liberation to coastal communities in Pemba, it should be readdressed to balance its economic values and services from seagrass.

Gut Microbiome Profiling of the Endangered Southern Greater Glider (Petauroides volans) after the 2019-2020 Australian Megafire.

Studying the gut microbiome can provide valuable insights into animal health and inform the conservation management of threatened wildlife. Gut microbiota play important roles in regulating mammalian host physiology, including digestion, energy metabolism and immunity. Dysbiosis can impair such physiological processes and compromise host health, so it is essential that the gut microbiome be considered in conservation planning. The southern greater glider (Petauroides volans) is an endangered arboreal marsupial that faced widespread habitat fragmentation and population declines following the 2019-2020 Australian bushfire season. This study details baseline data on the gut microbiome of this species. The V3-V4 region of the 16S rRNA gene was amplified from scats collected from individuals inhabiting burnt and unburnt sites across southeastern Australia and sequenced to determine bacterial community composition. Southern greater glider gut microbiomes were characterised by high relative abundances of Firmicutes and Bacteroidota, which is consistent with that reported for other marsupial herbivores. Significant differences in gut microbial diversity and community structure were detected among individuals from different geographic locations. Certain microbiota and functional orthologues were also found to be significantly differentially abundant between locations. The role of wildfire in shaping southern greater glider gut microbiomes was shown, with some significant differences in the diversity and abundance of microbiota detected between burnt and unburnt sites. Overall, this study details the first data on greater glider (Petauroides) gut microbiomes, laying the foundation for future studies to further explore relationships between microbial community structure, environmental stressors and host health.

The biotic ligand model as a promising tool to predict Cu toxicity in amazon blackwaters

The Rio Negro basin of Amazonia (Brazil) is a hotspot of fish biodiversity that is under threat from copper (Cu) pollution. The very ion-poor blackwaters have a high dissolved organic carbon (DOC) concentration. We investigated the Cu sensitivity of nine Amazonian fish species in their natural blackwaters (Rio Negro). The acute lethal concentration of Cu (96 h LC50) was determined at different dilutions of Rio Negro water (RNW) in ion-poor well water (IPW), ranging from 0 to 100%. The IPW was similar to RNW in pH and ionic composition but deficient in DOC, allowing this parameter to vary 20-fold from 0.4 to 8.3 mg/L in tests. The Biotic Ligand Model (BLM; Windward version 3.41.2.45) was used to model Cu speciation and toxicity over the range of tested water compositions, and to estimate lethal Cu accumulations on the gills (LA50). The modeling predicted a high relative abundance of Cu complexes with DOC in test waters. As these complexes became more abundant with increasing RNW content, a concomitant decrease in free Cu2+ was observed. In agreement with this modeling, acute Cu toxicity decreased (i.e. 96 h LC50 values increase) with increasing RNW content. The three most sensitive species (Hemigrammus rhodostomus, Carnegiella strigatta and Hyphessobrycon socolofi) were Characiformes, whereas Corydoras schwartzi (Siluriformes) and Apistogramma agassizii (Cichliformes) were the most tolerant. These sensitivity differences were reflected in the BLM-predicted lethal gill copper accumulation (LA50), which were generally lower in Characiformes than in Cichliformes. Using these newly estimated LA50 values in the BLM allowed for accurate prediction of acute Cu toxicity in the nine Amazonian fish. Our data emphasize that the BLM approach is a promising tool for assessing Cu risk to Amazonian fish species in blackwater conditions characterized by very low concentrations of major ions but high concentrations of DOC.

Optimization of methane production from co-digestion of citrus agro-industrial waste in a two-stage system: Investigation of the effects of organic matter concentration and alkalinization

The essential oils in citrus waste poses challenges for the anaerobic digestion application to energy recovery from these wastes due to the potential to inhibit the bioprocess. The two-stage system is a practical alternative to overcome these limitations of anaerobic co-digestion of citrus peel waste and wastewater. This study proposes to overcome drawbacks associated with the use of these substrates in anaerobic digestion by separating the phases, performing parameters optimization of the methanogenic stage. To obtain optimized conditions for the methanogenic stage, the Rotational Central Composite Design (RCCD) and Response Surface Methodology (RSM) were applied, evaluating the effects of diluting the Fermentation Reactor Content (FRC) of the first stage (35.7%–100%) and alkalinization (up to 0.60 g sodium bicarbonate.gCOD−1), in methane production and organic matter removal. Values from 2100.4 to 6320.6 mLCH4.L−1 were obtained in the experimental design assays, with no inhibition identified by the high substrate concentration, nor by the limonene content (1.5–5.0 mg.L−1). Lower dilution of the fermentation reactor content (90%–100%) resulted in higher accumulated methane production, while the variation in the alkalinization did not imply significant effects on this response. The optimized condition for maximum production potential was obtained with 99.3% of fermentation reactor content and 0.58 gNaCHO3.gCOD−1, reaching a production of 6549.7 mLCH4.L−1, with organic matter removal (rCOD) of 87.1%, and 58.6% of reduction in solid waste content. For this condition, acetogenic metabolism predominance was observed, in the conversion of butyric acid and propionic acid into acetic acid. In the analysis of the microbial community of the optimized condition assay, a high relative abundance of hydrolytic and acidogenic bacteria (AUTHM297, Lachnospiraceae, and Hungateiclostridiaceae) was observed, as well as methanogenic archaea related to acetoclastic, hydrogenotrophic, and methylotrophic methanogenesis (Methanoregula, Methanolinea, Methanomassiliicoccus, Candidatus Methanomethylicus, and Methanofolis).

Deciphering anaerobic ethanol metabolic pathways shaped by operational modes

Efficient anaerobic digestion requires the syntrophic cooperation among diverse microorganisms with various metabolic pathways. In this study, two operational modes, i.e., the sequencing batch reactor (SBR) and the continuous-flow reactor (CFR), were adopted in ethanol-fed systems with or without the supplement of powdered activated carbon (PAC) to examine their effects on ethanol metabolic pathways. Notably, the operational mode of SBR and the presence of CO2 facilitated ethanol metabolism towards propionate production. This was further evidenced by the dominance of Desulfobulbus, and the increased relative abundances of enzymes (EC: 1.2.7.1 and 1.2.7.11) involved in CO2 metabolism in SBRs. Moreover, SBRs exhibited superior biomass-based rates of ethanol degradation and methanogenesis, surpassing those in CFRs by 53.1% and 22.3%, respectively. Remarkably, CFRs with the extended solids retention time enriched high relative abundances of Geobacter of 71.7% and 70.4% under conditions with and without the addition of PAC, respectively. Although both long-term and short-term PAC additions led to the increased sludge conductivity and a reduced methanogenic lag phase, only the long-term PAC addition resulted in enhanced rates of ethanol degradation and propionate production/degradation. The strategies by adjusting operational mode and PAC addition could be adopted for modulating the anaerobic ethanol metabolic pathway and enriching Geobacter.

Co-digestion of solid-liquid waste from citrus agroindustrial: Effect of hydraulic retention time and organic loading rate on H2 production in a long-term continuous operation leach bed reactor

The Leach Bed Reactor (LBR) application is a promising alternative for the anaerobic digestion of solid waste and wastewater. In this study, the LBR was continuously operated for 160 days in four different phases, for co-fermentation of solid and liquid waste from the citrus agroindustry, at 37 °C, evaluating the effect of hydraulic retention time (HRT) and organic loading rate (OLR). The maximum volumetric hydrogen production (VHPR) was observed at an HRT of 12h (958.3 mLH2.L-1.d-1); however, the highest hydrogen yield (HY) was identified at an HRT of 24h (104.9 mLH2.g-1CHO). Based on the metabolic characteristics of microorganisms identified in higher relative abundance, by 16S rRNA sequencing, such as Lactobacillus, Caproicoproducens, Bifidobacterium, Olsenella, and Solobacterium, an occurrence of chain elongation pathways in the production of butyric and caproic acids was inferred, with hydrogen production resulting from the lactic acid oxidation. The maximum electricity production potential of 16.3 kWh.m-3 liquor was estimated.

Data mining reveals tissue-specific expression and host lineage-associated forms of Apis mellifera filamentous virus.

Apis mellifera filamentous virus (AmFV) is a large double-stranded DNA virus of uncertain phylogenetic position that infects honey bees (Apis mellifera). Little is known about AmFV evolution or molecular aspects of infection. Accurate annotation of open-reading frames (ORFs) is challenged by weak homology to other known viruses. This study was undertaken to evaluate ORFs (including coding-frame conservation, codon bias, and purifying selection), quantify genetic variation within AmFV, identify host characteristics that covary with infection rate, and examine viral expression patterns in different tissues. Short-read data were accessed from the Sequence Read Archive (SRA) of the National Center for Biotechnology Information (NCBI). Sequence reads were downloaded from accessions meeting search criteria and scanned for kmers representative of AmFV genomic sequence. Samples with kmer counts above specified thresholds were downloaded in full for mapping to reference sequences and de novo assembly. At least three distinct evolutionary lineages of AmFV exist. Clade 1 predominates in Europe but in the Americas and Africa it is replaced by the other clades as infection level increases in hosts. Only clade 3 was found at high relative abundance in hosts with African ancestry, whereas all clades achieved high relative abundance in bees of non-African ancestry. In Europe and Africa, clade 2 was generally detected only in low-level infections but was locally dominant in some North American samples. The geographic distribution of clade 3 was consistent with an introduction to the Americas with 'Africanized' honey bees in the 1950s. Localized genomic regions of very high nucleotide divergence in individual isolates suggest recombination with additional, as-yet unidentified AmFV lineages. A set of 155 high-confidence ORFs was annotated based on evolutionary conservation in six AmFV genome sequences representative of the three clades. Pairwise protein-level identity averaged 94.6% across ORFs (range 77.1-100%), which generally exhibited low evolutionary rates and moderate to strong codon bias. However, no robust example of positive diversifying selection on coding sequence was found in these alignments. Most of the genome was detected in RNA short-read alignments. Transcriptome assembly often yielded contigs in excess of 50 kb and containing ORFs in both orientations, and the termini of long transcripts were associated with tandem repeats. Lower levels of AmFV RNA were detected in brain tissue compared to abdominal tissue, and a distinct set of ORFs had minimal to no detectable expression in brain tissue. A scan of DNA accessions from the parasitic mite Varroa destructor was inconclusive with respect to replication in that species. Collectively, these results expand our understanding of this enigmatic virus, revealing transcriptional complexity and co-evolutionary associations with host lineage.

Evaluating the Ileal and Cecal Microbiota Composition of a 1940 Heritage Genetic Line and a 2016 Commercial Line of white Leghorns Fed Representative Diets from 1940 to 2016

This study identified and evaluated differences between microbiome compositions of the ileum and ceca of 1940 and 2016 white leghorn genetic strains fed representative contemporary diets from those times. Ileal and cecal samples were collected at 69 weeks of age. Alpha and beta diversity metrics were generated, and the Analysis of Composition of Microbiomes (ANCOM) was utilized to determine significantly different taxa. Ileum and ceca alpha diversity were significantly different (p = 0.001; Q = 0.001); however, no differences between genetic lineage were observed (p > 0.05; Q > 0.05). Beta diversity between the ileum and ceca and the genetic lines was significantly different (p = 0.001; Q = 0.001). The ANCOM of the ileum showed significant differences between Proteobacteria and Actinobacteriota phyla (p ˂ 0.05) and significant differences between Pseudomonas, Rhizobiaceae, Leuconostoc, and Aeriscardovia genera (p ˂ 0.05). For ceca ANCOM, Proteobacteria, Firmicutes, Actinobacteriota, and Euryarchaeota phyla were significantly different (p ˂ 0.05), with Firmicutes having the highest relative abundance across all groups, and there were significant differences in genera Pseudomonas, Leuconostoc, Alloprevotella, and Aeri scardovia, with Alloprevotella having the highest relative abundance. The results suggest that genetic makeup in conjunction with the nutritional composition influences the cecal and ileal microbiota of corresponding hens.

Phylogenomic position of genetically diverse phagotrophic stramenopile flagellates in the sediment-associated MAST-6 lineage and a potentially halotolerant placididean

Unlike morphologically conspicuous ochrophytes, many flagellates belonging to basally branching stramenopiles are small and often overlooked. As a result, many of these lineages are known only through molecular surveys and identified as MArine STramenopiles (MAST), and remain largely uncharacterized at the cellular or genomic level. These likely phagotrophic flagellates are not only phylogenetically diverse, but also extremely abundant in some environments, making their characterization all the more important. MAST-6 is one example of a phylogenetically distinct group that has been known to be associated with sediments, but little else is known about it. Indeed, until the present study, only a single species from this group, Pseudophyllomitus vesiculosus (Pseudophyllomitidae), has been both formally described and associated with genomic information. Here, we describe four new species including two new genera of sediment-dwelling MAST-6, Vomastramonas tehuelche gen. et sp. nov., Mastreximonas tlaamin gen. et sp. nov., one undescribed Pseudophyllomitus sp., BSC2, and a new species belonging to Placididea, the potentially halotolerant Haloplacidia sinai sp. nov. We also provide two additional bikosian transcriptomes from a public culture collection, to allow for better phylogenetic reconstructions of deep-branching stramenopiles. With the SSU rRNA sequences of the new MAST-6 species, we investigate the phylogenetic diversity of the MAST-6 group and show a high relative abundance of MAST-6 related to M. tlaamin in samples across various depths and geographical locations. Using the new MAST-6 species, we also update the phylogenomic tree of stramenopiles, particularly focusing on the paraphyly of Bigyra.