Core Bacteria Research Articles

Exploring the Core Bacteria and Functional Traits in Pecan (Carya illinoinensis) Rhizosphere.

Pecan (Carya illinoinensis) and Chinese hickory (Carya cathayensis) are important commercially cultivated nut trees. They are phylogenetically closely related plants; however, they exhibit significantly different phenotypes in response to abiotic stress and development. The rhizosphere selects core microorganisms from bulk soil, playing a pivotal role in the plant's resistance to abiotic stress and growth. In this study, we used metagenomic sequencing to compare the selection capabilities of seedling pecan and seedling hickory at taxonomic and functional levels in bulk soil and the rhizosphere. We observed that pecan has a stronger capacity to enrich rhizosphere plant-beneficial microbe bacteria (e.g., Rhizobium, Novosphingobium, Variovorax, Sphingobium, and Sphingomonas) and their associated functional traits than hickory. We also noted that the ABC transporters (e.g., monosaccharide transporter) and bacterial secretion systems (e.g., type IV secretion system) are the core functional traits of pecan rhizosphere bacteria. Rhizobium and Novosphingobium are the main contributors to the core functional traits. These results suggest that monosaccharides may help Rhizobium to efficiently enrich this niche. Novosphingobium may use a type IV secretion system to interact with other bacteria and thereby influence the assembly of pecan rhizosphere microbiomes. Our data provide valuable information to guide core microbial isolation and expand our knowledge of the assembly mechanisms of plant rhizosphere microbes. IMPORTANCE The rhizosphere microbiome has been identified as a fundamental factor in maintaining plant health, helping plants to fight the deleterious effects of diseases and abiotic stresses. However, to date, studies on the nut tree microbiome have been scarce. Here, we observed a significant "rhizosphere effect" on the seedling pecan. We furthermore demonstrated the core rhizosphere microbiome and function in the seedling pecan. Moreover, we deduced possible factors that help the core bacteria, such as Rhizobium, to efficiently enrich the pecan rhizosphere and the importance of the type IV system for the assembly of pecan rhizosphere bacterial communities. Our findings provide information for understanding the mechanism of the rhizosphere microbial community enrichment process.

Characterization of prophages in bacterial genomes from the honey bee (Apis mellifera) gut microbiome.

The gut of the European honey bee (Apis mellifera) possesses a relatively simple bacterial community, but little is known about its community of prophages (temperate bacteriophages integrated into the bacterial genome). Although prophages may eventually begin replicating and kill their bacterial hosts, they can also sometimes be beneficial for their hosts by conferring protection from other phage infections or encoding genes in metabolic pathways and for toxins. In this study, we explored prophages in 17 species of core bacteria in the honey bee gut and two honey bee pathogens. Out of the 181 genomes examined, 431 putative prophage regions were predicted. Among core gut bacteria, the number of prophages per genome ranged from zero to seven and prophage composition (the compositional percentage of each bacterial genome attributable to prophages) ranged from 0 to 7%. Snodgrassella alvi and Gilliamella apicola had the highest median prophages per genome (3.0 ± 1.46; 3.0 ± 1.59), as well as the highest prophage composition (2.58% ± 1.4; 3.0% ± 1.59). The pathogen Paenibacillus larvae had a higher median number of prophages (8.0 ± 5.33) and prophage composition (6.40% ± 3.08) than the pathogen Melissococcus plutonius or any of the core bacteria. Prophage populations were highly specific to their bacterial host species, suggesting most prophages were acquired recently relative to the divergence of these bacterial groups. Furthermore, functional annotation of the predicted genes encoded within the prophage regions indicates that some prophages in the honey bee gut encode additional benefits to their bacterial hosts, such as genes in carbohydrate metabolism. Collectively, this survey suggests that prophages within the honey bee gut may contribute to the maintenance and stability of the honey bee gut microbiome and potentially modulate specific members of the bacterial community, particularly S. alvi and G. apicola.

Microbial metabolism and humic acid formation in response to enhanced copper and zinc passivation during composting of wine grape pomace and pig manure

Copper (Cu) and zinc (Zn) in piglet feed can lead to heavy metals (HMs) accumulation in pig manure (PM). Composting is crucial for recycling biowaste and decreasing HMs bioavailability. This study aimed to investigate the impact of adding wine grape pomace (WGP) on the bioavailability of HMs during PM composting. WGP facilitated the passivation of HMs through Cytophagales and Saccharibacteria_genera_incertae_sedis which promoted the formation of humic acid (HA). Polysaccharide and aliphatic groups in HA dominated the transformation of chemical forms of HMs. Moreover, adding 60% and 40% WGP enhanced the Cu and Zn passivation effects by 47.24% and 25.82%, respectively. Polyphenol conversion rate and core bacteria were identified as key factors in affecting HMs passivation. These results offered new insights into the fate of HMs during PM composting in response to the addition of WGP, which is helpful to practical application of WGP to inactivate HMs for improving compost quality.

Epiphytic common core bacteria in the microbiomes of co-located green (Ulva), brown (Saccharina) and red (Grateloupia, Gelidium) macroalgae

BackgroundMacroalgal epiphytic microbial communities constitute a rich resource for novel enzymes and compounds, but studies so far largely focused on tag-based microbial diversity analyses or limited metagenome sequencing of single macroalgal species.ResultsWe sampled epiphytic bacteria from specimens of Ulva sp. (green algae), Saccharina sp. (brown algae), Grateloupia sp. and Gelidium sp. (both red algae) together with seawater and sediment controls from a coastal reef in Weihai, China, during all seasons. Using 16S rRNA amplicon sequencing, we identified 14 core genera (consistently present on all macroalgae), and 14 dominant genera (consistently present on three of the macroalgae). Core genera represented ~ 0.7% of all genera, yet accounted for on average 51.1% of the bacterial abundances. Plate cultivation from all samples yielded 5,527 strains (macroalgae: 4,426) representing 1,235 species (685 potentially novel). Sequencing of selected strains yielded 820 non-redundant draft genomes (506 potentially novel), and sequencing of 23 sampled metagenomes yielded 1,619 metagenome-assembled genomes (MAGs), representing further 1,183 non-redundant genomes. 230 isolates and 153 genomes were obtained from the 28 core/dominant genera. We analyzed the genomic potential of phycosphere bacteria to degrade algal polysaccharides and to produce bioactive secondary metabolites. We predicted 4,451 polysaccharide utilization loci (PULs) and 8,810 biosynthetic gene clusters (BGCs). These were particularly prevalent in core/dominant genera.ConclusionsOur metabolic annotations and analyses of MAGs and genomes provide new insights into novel species of phycosphere bacteria and their ecological niches for an improved understanding of the macroalgal phycosphere microbiome.DnRc39z963CYrL7RdN5UNdVideo

Effects of adding corn steep liquor on bacterial community composition and carbon and nitrogen transformation during spent mushroom substrate composting

BackgroundCarbon and nitrogen are essential energy and nutrient substances in the composting process. Corn steep liquor (CSL) is rich in soluble carbon and nitrogen nutrients and active substances and is widely used in the biological industry. Nonetheless, limited research has been done on the effect of CSL on composting. This work firstly reveals the effect of adding CSL to bacterial community composition and carbon and nitrogen conversion during composting. This study provides the choice of auxiliary materials for the spent mushroom substrate compost (SMS) and some novel knowledge about the effect of bacterial community on C and N cycling during composting of SMS and CSL. Two treatments were set up in the experiment: 100% spent mushroom substrate (SMS) as CK and SMS + 0.5% CSL (v/v) as CP.ResultsThe results showed that the addition of CSL enhanced the initial carbon and nitrogen content of the compost, altered the bacterial community structure, and increased the bacterial diversity and relative abundance, which might be beneficial to the conversion and retention of carbon and nitrogen in the composting process. In this paper, network analysis was used to screen the core bacteria involved in carbon and nitrogen conversion. In the CP network, the core bacteria were divided into two categories, synthesizing and degrading bacteria, and there were more synthesizing bacteria than degrading bacteria, so the degradation and synthesis of organic matter were carried out simultaneously, while only degrading bacteria were found in the CK network. Functional prediction by Faprotax identified 53 groups of functional bacteria, among which 20 (76.68% abundance) and 14 (13.15% abundance) groups of functional bacteria were related to carbon and nitrogen conversion, respectively. Adding CSL stimulated the compensatory effect of core and functional bacteria, enhanced the carbon and nitrogen transformation ability, stimulated the activity of low-abundance bacteria, and reduced the competitive relationship between the bacterial groups. This may be why the addition of CSL accelerated the organic matter degradation and increased carbon and nitrogen preservation.ConclusionsThese findings indicate that the addition of CSL promoted the cycling and preservation of carbon and nitrogen in the SMS composts, and the addition of CSL to the compost may be an effective way to dispose of agricultural waste.

Potential values of formalin-fixed paraffin-embedded tissues for intratumoral microbiome analysis in breast cancer

Breast cancer (BC) tissues have been proved to harbor microorganisms, which could potentially contribute to oncogenesis. Formalin-fixed paraffin-embedded (FFPE) tissues are the most widespread clinical samples in BC research. To verify the potential of FFPE tissues in microbiological analysis, we analyzed the microbial communities of FFPE and fresh frozen (FF) tumor samples from 30 participants diagnosed with BC deploying 16S rRNA sequencing. The operational taxonomic units (OTUs) analysis showed that 78.55% of OTUs in FFPE samples were consistent with FF samples. The composition of core bacteria did not change much, and there is also no difference in alpha diversity between FFPE and FF (without unclassified bacteria). Taxonomic variation results show that Firmicutes and Bacteroidota phyla, and their major classes, maintained the same proportion under two preservation methods. In addition, the major class Gammaproteobacteria, as well as its dominant orders Burkholderiales and Pseudomonadales all showed no significant difference in paired analysis. Moreover, the Proteobacteria and Actinobacteriota phyla showed no significant difference between FFPE and FF samples after subtracting unclassified bacteria. Therefore, premised with the intrinsic tumor heterogeneity and unclassified bacteria, there are potential values of FFPE tissues for intratumoral microbiome analysis in breast cancer.

Hydrochemical characteristics and microbial community evolution of Pinglu River affected by regional abandoned coal mine drainage, Guizhou Province, China.

Pinglu River in southwestern China was continuously polluted by acid mine drainage (AMD) from abandoned coal mines, and AMD has become a major source of recharge to the river (43.26% of total flow), resulting in structural changes in the physicochemical properties and microbial communities of river water and sediments. In this study, we collected abandoned coal mine drainage, river water, and river sediment samples for comprehensive analysis. Results indicated that the hydrochemical types of AMD from abandoned coal mines were mainly SO4-Ca·Mg. The pH of river water in Pinglu River decreased from upstream to downstream due to AMD, with the hydrochemical type gradually changing from SO4·HCO3-Ca·Mg to SO4-Ca·Mg. The variation of pH along the river sediments was less than that of water samples, which remained weakly alkaline. However, high-throughput sequencing revealed a gradual decrease in microbial diversity in river sediments from upstream to downstream. The core bacteria groups in the upstream sediments were mainly attributed to the phylum Proteobacteria and Actinobacteriota, mainly including Geobacter, Anaeromyxobacter, Marmoricola, and Phycicoccus. The relative abundance of Gaiella, MND1, and Pseudolabrys in sediment samples gradually increased with the confluence of AMD, and the differences in microbial communities may be attributed to pH, TOC, and TP. Results of phenotype prediction demonstrated that the relative abundance of anaerobic microorganisms in river sediment gradually decreased from upstream to downstream (from 24.77 to 12.46%), presumably due to the large amount of oligotrophic AMD converge.

A core of functional complementary bacteria infects oysters in Pacific Oyster Mortality Syndrome

BackgroundThe Pacific oyster Crassostrea gigas is one of the main cultivated invertebrate species worldwide. Since 2008, oyster juveniles have been confronted with a lethal syndrome known as the Pacific Oyster Mortality Syndrome (POMS). POMS is a polymicrobial disease initiated by a primary infection with the herpesvirus OsHV-1 µVar that creates an oyster immunocompromised state and evolves towards a secondary fatal bacteremia.ResultsIn the present article, we describe the implementation of an unprecedented combination of metabarcoding and metatranscriptomic approaches to show that the sequence of events in POMS pathogenesis is conserved across infectious environments. We also identified a core bacterial consortium which, together with OsHV-1 µVar, forms the POMS pathobiota. This bacterial consortium is characterized by high transcriptional activities and complementary metabolic functions to exploit host’s resources. A significant metabolic specificity was highlighted at the bacterial genus level, suggesting low competition for nutrients between members of the core bacteria.ConclusionsLack of metabolic competition between the core bacteria might favor complementary colonization of host tissues and contribute to the conservation of the POMS pathobiota across distinct infectious environments.

Response characteristics of flax retting liquid addition during chicken manure composting: Focusing on core bacteria in organic carbon mineralization and humification

To explore the applicability of flax retting liquid (FRL) addition, the physicochemical properties, microbial community structure and function, carbon conversion and humus (HS) formation were assessed during chicken manure (CM) aerobic composting. Compared with the control group, the addition of FRL increased the temperature at thermophilic phase, while the microbial mass carbon content (MBC) in SCF and FRH groups raised to 96.1 ± 0.25 g/Kg and 93.33 ± 0.27 g/Kg, respectively. Similarly, FRL also improved the concent of humic acid (HA) to 38.44 ± 0.85 g/Kg, 33.06 ± 0.8 g/Kg, respcetively. However, fulvic acid (FA) decreased to 30.02 ± 0.55 g/Kg, 31.4 ± 0.43 g/Kg, respectively and further reduced CO2 emissions. FRL influenced the relative abundance of Firmicutes at thermophilic phase and Ornithinimicrobium at maturity phase. Additionally, FRL strengthen the association among flora and reduce the number of bacteria, which was negative correlated with HA and positive with CO2 during composting. These findings offer powerful technological support for improving agricultural waste recycling.

Time series cluster analysis reveals individual assignment of microbiota in captive tiger (Panthera tigris) and wildebeest (Connochaetes taurinus).

Fecal microbiota variability and individuality are well studied in humans and also in farm animals (related to diet- or disease-specific influences), but very little is known for exotic zoo-housed animals. This includes a wide range of species that differ greatly in microbiota composition and variation. For example, herbivorous species show a very similar and constant fecal microbiota over time, whereas carnivorous species appear to be highly variable in fecal microbial diversity and composition. Our objective was to determine whether species-specific and individual-specific clustering patterns were observed in the fecal microbiota of wildebeest (Connochaetes taurinus) and tigers (Panthera tigris). We collected 95 fecal samples of 11 animal individuals that were each sampled over eight consecutive days and analyzed those with Illumina MiSeq sequencing of the V3-V4 region of the 16SrRNA gene. In order to identify species or individual clusters, we applied two different agglomerative hierarchical clustering algorithms - a community detection algorithm and Ward's linkage. Our results showed that both, species-specific and individual-specific clustering is possible, but more reliable results were achieved when applying dynamic time warping which finds the optimal alignment between different time series. Furthermore, the bacterial families that distinguish individuals from each other in both species included daily occurring core bacteria (e.g., Acidaminococcaceae in wildebeests or Clostridiaceae in tigers) as well as individual dependent and more fluctuating bacterial families. Our results suggest that while it is necessary to consider multiple consecutive samples per individual, it is then possible to characterize individual abundance patterns in fecal microbiota in both herbivorous and carnivorous species. This would allow establishing individual microbiota profiles of animals housed in zoos, which is a basic prerequisite to quickly detect deviations and use microbiome analysis as a non-invasive and cost-effective tool in animal welfare.

The driving mechanism of passivator islands adsorbing and immobilizing heavy metals during chicken manure composting

The aim of this study was to assess the effectiveness of biochar and montmorillonite islands on heavy metal adsorptive immobilization and identify crucial driving factors and pathways during chicken manure composting. Compared to montmorillonite (6.74 and 89.25 mg/kg), biochar exhibited an obviously higher ability of Cu and Zn enrichment (41.79 and 167.77 mg/kg), might be attributed to its abundant active functional groups. Network analysis showed that compared to Cu, core bacteria positively and negatively related to Zn was obviously more and less in passivator islands, respectively, which might explain significantly higher Zn concentration. Structural Equation Model displayed that dissolved organic carbon (DOC), pH and bacteria were critical driving factors. Pretreatment of passivator packages, such as soaking in the solution being rich in DOC and inoculating specific microbial agents accumulating heavy metals via extracellular adsorption /intracellular interception would significantly improve the effectiveness of adsorptive passivation on heavy metals.

Phylogenetic distance affects the artificial microbial consortia’s effectiveness and colonization during the bioremediation of polluted soil with Cr(VI) and atrazine

Soils co-contaminated with heavy metals and organic pollutants are common and threaten the natural environment and human health. Although artificial microbial consortia have advantages over single strains, the mechanism affecting their effectiveness and colonization in polluted soils still requires determination. Here, we constructed two kinds of artificial microbial consortia from the same or different phylogenetic groups and inoculated them into soil co-contaminated with Cr(VI) and atrazine to study the effects of phylogenetic distance on consortia effectiveness and colonization. The residual concentrations of pollutants demonstrated that the artificial microbial consortium from different phylogenetic groups achieved the highest removal rates of Cr(VI) and atrazine. The removal rate of 400 mg/kg atrazine was 100%, while that of 40 mg/kg Cr(VI) was 57.7%. High-throughput sequence analysis showed that the soil bacterial negative correlations, core genera, and potential metabolic interactions differed among treatments. Furthermore, artificial microbial consortia from different phylogenetic groups had better colonization and a more significant effect on the abundance of native core bacteria than consortia from the same phylogenetic group. Our study highlights the importance of phylogenetic distance on consortium effectiveness and colonization and offers insight into the bioremediation of combined pollutants.

The reverse function of lignin-degrading enzymes: The polymerization ability to promote the formation of humic substances in domesticated composting

This study aimed to confirm the ability of lignin peroxidase (LiP) and manganese peroxidase (MnP) in promoting the formation of humic substances (HS) during domesticated composting. Three raw materials with different lignin types were used for composting, including rice straw, tree branches, and pine needles. Results suggested that LiP and MnP activity increased during domesticated composting. But HS formation was only promoted by LiP. The effect of MnP was insignificant, which might be caused by the lack of enzyme cofactors like Mn2+. Meanwhile, bacteria highly associated with LiP and MnP production were identified as core bacteria. Function prediction of 16S-PICRUSt2 showed that the function of core bacteria was consistent with total bacterial functions which mainly promoted compost humification. Therefore, it speculated that LiP and MnP had the ability to promote HS formation during composting. Accordingly, it is a new understanding of the role of biological enzymes in composting.

Exploration of microbiome diversity of stacked fermented grains by flow cytometry and cell sorting.

Sauce-flavor baijiu is one of the twelve flavor types of Chinese distilled fermented product. Microbial composition plays a key role in the stacked fermentation of Baijiu, which uses grains as raw materials and produces flavor compounds, however, the active microbial community and its relationship remain unclear. Here, we investigated the total and active microbial communities of stacked fermented grains of sauce-flavored Baijiu using flow cytometry and high-throughput sequencing technology, respectively. By using traditional high-throughput sequencing technology, a total of 24 bacterial and 14 fungal genera were identified as the core microbiota, the core bacteria were Lactobacillus (0.08-39.05%), Acetobacter (0.25-81.92%), Weissella (0.03-29.61%), etc. The core fungi were Issatchenkia (23.11-98.21%), Monascus (0.02-26.36%), Pichia (0.33-37.56%), etc. In contrast, using flow cytometry combined with high-throughput sequencing, the active dominant bacterial genera after cell sorting were found to be Herbaspirillum, Chitinophaga, Ralstonia, Phenylobacterium, Mucilaginibacter, and Bradyrhizobium, etc., whereas the active dominant fungal genera detected were Aspergillus, Pichia, Exophiala, Candelabrochaete, Italiomyces, and Papiliotrema, etc. These results indicate that although the abundance of Acetobacter, Monascus, and Issatchenkia was high after stacked fermentation, they may have little biological activity. Flow cytometry and cell sorting techniques have been used in the study of beer and wine, but exploring the microbiome in such a complex environment as Chinese baijiu has not been reported. The results also reveal that flow cytometry and cell sorting are convenient methods for rapidly monitoring complex microbial flora and can assist in exploring complex environmental samples.

Relation analysis of bacterial community in soils of coal mines with potential ecological risk from heavy metals

Coal consumption increases consistently, and heavy metal contamination in soils surrounding coal mines has been a severe environmental issue. Investigation of the relations of the bacterial community in soils of coal mines with potential ecological risk from heavy metals is essential for better understanding the impact of coal production on ecosystem health. In this study, soils surrounding two coal mines in a typical coal industry city of China were sampled, and heavy metals (Cd, Cr, Ni, Cu, Zn, As, and Pb) were quantified together with an in-depth evaluation of bacterial community based on high-throughput sequencing. The individual and overall ecological risk from heavy metals were estimated, and their relations with the identified seven core bacteria were analyzed. For soils surrounding both coal mines, in phylum level, five dominant bacterial taxa (Proteobacteria, Acidobacteriota, Actinobacteria, Firmicutes, and Bacteroidota) were identified, and their differences in relative abundance were clearly revealed, even if the differences between the two mines were not significant. When evaluated in genus level, apparent differences in bacterial community structure and complexity were found. The soils with higher potential ecological risk showed relatively lower complexity for the bacterial community. Seven core bacteria were identified, and negative relations of their relative abundance with the individual and overall ecological risk from heavy metals were revealed. Two families (Halomonadaceae and Aeromonadaceae) and two genera (Oceanisphaera and Ignatzschineria) were found more sensitive to both the individual risk from arsenic and the overall risk from all heavy metals, suggesting their possibility as indicators of soil contamination by these metal elements. Different from these, Rhizobiaceae revealed a positive relation with the overall risk value, implying their strong tolerance to heavy metals and, therefore, possible effect in bioremediation and phytoremediation of heavy metal contaminated soils. These findings have great reference value for better understanding the impacts of heavy metal contamination induced by coal production.

Different ratios of raw material triggered composting maturity associated with bacterial community co-occurrence patterns

Exploring the ecological function of potential core bacteria for high-efficiency composting can provide a fundamental understanding of the role of composting bacterial communities. Mushroom residue and kitchen garbage at different ratios (N1: 1/1, N2: 1/2) of dry weight were tested to investigate the key ecological role of the core bacteria responsible for producing mature compost. N1 had a peak temperature of 75.0 °C which was higher than N2 (68.3 °C). Other key composting parameters (carbon to nitrogen ratio (C/N) and germination index (GI)) also indicated that N1 achieved higher compost maturity. Rice seedlings experiments also further validated this conclusion. Putative key bacterial taxa (Thermobifida, Luteimonasd, Bacillus, etc.) were positively associated with the GI, indicating a substantial contribution to composting maturity. Co-occurrence network analysis revealed the ecological function of potentially beneficial core bacteria promoted cooperation among the bacterial community. The putative core bacteria in N1 may affect composting efficiency. Our findings reveal the mechanism of potential core bacteria throughout the compost maturity phases.

Microbial diversity and metabolic function in duodenum, jejunum and ileum of emu (Dromaius novaehollandiae)

Emus (Dromaius novaehollandiae), a large flightless omnivorous ratite, are farmed for their fat and meat. Emu fat can be rendered into oil for therapeutic and cosmetic use. They are capable of gaining a significant portion of its daily energy requirement from the digestion of plant fibre. Despite of its large body size and low metabolic rate, emus have a relatively simple gastroinstetinal (GI) tract with a short mean digesta retention time. However, little is known about the GI microbial diversity of emus. The objective of this study was to characterize the intraluminal intestinal bacterial community in the different segments of small intestine (duodenum, jejunum, and ileum) using pyrotag sequencing and compare that with the ceca. Gut content samples were collected from each of four adult emus (2 males, 2 females; 5–6 years old) that were free ranged but supplemented with a barley-alfalfa-canola based diet. We amplified the V3-V5 region of 16S rRNA gene to identify the bacterial community using Roche 454 Junior system. After quality trimming, a total of 165,585 sequence reads were obtained from different segments of the small intestine (SI). A total of 701 operational taxonomic units (OTUs) were identified in the different segments of small intestine. Firmicutes (14–99%) and Proteobacteria (0.5–76%) were the most predominant bacterial phyla in the small intestine. Based on species richness estimation (Chao1 index), the average number of estimated OTUs in the small intestinal compartments were 148 in Duodenum, 167 in Jejunum, and 85 in Ileum, respectively. Low number of core OTUs identified in each compartment of small intestine across individual birds (Duodenum: 13 OTUs, Jejunum: 2 OTUs, Ileum: 14 OTUs) indicated unique bacterial community in each bird. Moreover, only 2 OTUs (Escherichia and Sinobacteraceae) were identified as core bacteria along the whole small intestine. PICRUSt analysis has indicated that the detoxification of plant material and environmental chemicals seem to be performed by SI microbiota, especially those in the jejunum. The emu cecal microbiome has more genes than SI segments involving in protective or immune response to enteric pathogens. Microbial digestion and fermentation is mostly in the jejunum and ceca. This is the first study to characterize the microbiota of different compartments of the emu intestines via gut samples and not fecal samples. Results from this study allow us to further investigate the influence of the seasonal and physiological changes of intestinal microbiota on the nutrition of emus and indirectly influence the fatty acid composition of emu fat.

Effects of Biological Nitrification Inhibitor on Nitrous Oxide and nosZ, nirK, nirS Denitrifying Bacteria in Paddy Soils

This study aimed to investigate the effects of a biological nitrification inhibitor on nitrous oxide emission and rice yield quality in paddy soils and its effects on denitrifying the bacteria of nosZ, nirK, and nirS types. Two treatments were performed: (1) using a local conventional fertilizer as the control CK; (2) using the partial application of a conventional fertilizer + biological nitrification inhibitor as SW. N2O emission was measured using gas chromatography; qPCR amplification was performed using primers for the targeted functional genes, nosZ, nirS, and nirK, and denitrifying functional gene abundance and denitrifying microbial community structure were analyzed using fluorescence quantification and high–throughput sequencing, respectively. The results reveal that the biological nitrification inhibitor resulted in a 41.83% reduction in N2O, relative to the normal fertilizer treatment. Meanwhile, rice yield increased by 15.45% and related quality indexes were also improved. This can promote the reproduction of bacteria with the nosZ gene while inhibiting the growth of bacteria with nirS and nirK genes. The core bacteria, Nitrosospira, Rhodanobacter, Bradyrhizobium, Tardiphaga, Rhodopseudomonas, and Paracoccus, positively correlated with N2O emissions, while core bacteria Azospirillum, Burkholderia, and Mesorhizobium negatively correlated with N2O emissions. Therefore, the application of a biological nitrification inhibitor could be an effective measure to promote rice yield and quality, reduce N2O emissions, and affect key denitrifying bacteria.

Enhancing quorum quenching media with 3D robust electrospinning coating: A novel biofouling control strategy for membrane bioreactors

Bacterial quorum quenching (QQ) is an effective strategy for controlling biofouling in membrane bioreactor (MBR) by interfering the releasing and degradation of signal molecules during quorum sensing (QS) process. However, due to the framework feature of QQ media, the maintenance of QQ activity and the restriction of mass transfer threshold, it has been difficult to design a more stable and better performing structure in a long period of time. In this research, electrospun fiber coated hydrogel QQ beads (QQ-ECHB) were fabricated by using electrospun nanofiber coated hydrogel to strengthen layers of QQ carriers for the first time. The robust porous PVDF 3D nanofiber membrane was coated on the surface of millimeter-scale QQ hydrogel beads. Biocompatible hydrogel entrapping quorum quenching bacteria (sp.BH4) was employed as the core of the QQ-ECHB. In MBR with the addition of QQ-ECHB, the time to reach transmembrane pressure (TMP) of 40 kPa was 4 times longer than conventional MBR. The robust coating and porous microstructure of QQ-ECHB contributed to keeping a lasting QQ activity and stable physical washing effect at a very low dosage (10g beads/5L MBR). Physical stability and environmental-tolerance tests also verified that the carrier can maintain the structural strength and keep the core bacteria stable when suffering long-term cyclic compression and great fluctuations in sewage quality.

Diet and high altitude strongly drive convergent adaptation of gut microbiota in wild macaques, humans, and dogs to high altitude environments.

Animal gut microbiota plays an indispensable role in host adaptation to different altitude environments. At present, little is known about the mechanism of animal gut microbiota in host adaptation to high altitude environments. Here, we selected wild macaques, humans, and dogs with different levels of kinship and intimate relationships in high altitude and low altitude environments, and analyzed the response of their gut microbiota to the host diet and altitude environments. Alpha diversity analysis found that at high altitude, the gut microbiota diversity of wild macaques with more complex diet in the wild environments is much higher than that of humans and dogs with simpler diet (p < 0.05), and beta diversity analysis found that the UniFrac distance between humans and dogs was significantly lower than between humans and macaques (p < 0.05), indicating that diet strongly drive the convergence of gut microbiota among species. Meanwhile, alpha diversity analysis found that among three subjects, the gut microbiota diversity of high altitude population is higher than that of low altitude population (ACE index in three species, Shannon index in dog and macaque and Simpson index in dog, p < 0.05), and beta diversity analysis found that the UniFrac distances among the three subjects in the high altitude environments were significantly lower than in the low altitude environments (p < 0.05). Additionally, core shared ASVs analysis found that among three subjects, the number of core microbiota in high altitude environments is higher than in low altitude environments, up to 5.34 times (1,105/207), and the proportion and relative abundance of the core bacteria types in each species were significantly higher in high altitude environments than in low altitude environments (p < 0.05). The results showed that high altitude environments played an important role in driving the convergence of gut microbiota among species. Furthermore, the neutral community model trial found that the gut microbiota of the three subjects was dispersed much more at high altitude than at low altitude, implying that the gut microbiota convergence of animals at high altitudes may be partly due to the microbial transmission between hosts mediated by human activities.