Number Of Operational Taxonomic Units Research Articles

Bladder Microbiota Are Associated with Clinical Conditions That Extend beyond the Urinary Tract.

Background. Since the discovery of the human urinary microbiota (UM), alterations in microbial community composition have been associated with various genitourinary conditions. The aim of this exploratory study was to examine possible associations of UM with clinical conditions beyond the urinary tract and to test some of the conclusions from previous studies on UM. Methods. Catheterised urine samples from 87 men were collected prior to endoscopic urological interventions under anaesthesia. The composition of the bacterial community in urine was characterized using the hypervariable V4 region of the 16S rRNA gene. Samples from 58 patients yielded a sufficient amount of bacterial DNA for analysis. Alpha diversity measures (number of operational taxonomic units, ACE, iChao2, Shannon and Simpson indices) were compared with the Kruskal–Wallis test. Beta diversity (differences in microbial community composition) was assessed using non-metric dimensional scaling in combination with the Prevalence in Microbiome Analysis algorithm. Results. Differences in bacterial richness and diversity were observed for the following variables: age, diabetes mellitus, dyslipidemia, smoking status and single-dose preoperative antibiotics. Differences in microbial community composition were observed in the presence of chronic kidney disease, lower urinary tract symptoms and antibiotic prophylaxis. Conclusions. UM appears to be associated with certain clinical conditions, including those unrelated to the urinary tract. Further investigation is needed before conclusions can be drawn for diagnostics and treatment.

DNA barcoding for biodiversity assessment: Croatian stoneflies (Insecta: Plecoptera).

BackgroundThe hemi-metabolous aquatic order Plecoptera (stoneflies) constitutes an indispensable part of terrestrial and aquatic food webs due to their specific life cycle and habitat requirements. Stoneflies are considered one of the most sensitive groups to environmental changes in freshwater ecosystems and anthropogenic changes have caused range contraction of many species. Given the critical threat to stoneflies, the study of their distribution, morphological variability and genetic diversity should be one of the priorities in conservation biology. However, some aspects about stoneflies, especially a fully resolved phylogeny and their patterns of distribution are not well known. A study that includes comprehensive field research and combines morphological and molecular identification of stoneflies has not been conducted in Croatia so far. Thus, the major aim of this study was to regenerate a comprehensive and taxonomically well-curated DNA barcode database for Croatian stoneflies, to highlight the morphological variability obtained for several species and to elucidate results in light of recent taxonomy.MethodsA morphological examination of adult specimens was made using basic characteristics for distinguishing species: terminalia in males and females, head and pronotum patterns, penial morphology, and egg structures. DNA barcoding was applied to many specimens to help circumscribe known species, identify cryptic or yet undescribed species, and to construct a preliminary phylogeny for Croatian stoneflies.ResultsSequences (658 bp in length) of 74 morphospecies from all families present in Croatia were recovered from 87% of the analysed specimens (355 of 410), with one partial sequence of 605 bp in length for Capnopsis schilleri balcanica Zwick, 1984. A total of 84% morphological species could be unambiguously identified using COI sequences. Species delineation methods confirmed the existence of five deeply divergent genetic lineages, with monophyletic origin, which also differ morphologically from their congeners and represent distinct entities. BIN (Barcode Index Number) assignment and species delineation methods clustered COI sequences into different numbers of operational taxonomic units (OTUs). ASAP delimited 76 putative species and achieved a maximum match score with morphology (97%). ABGD resulted in 62 and mPTP in 61 OTUs, indicating a more conservative approach. Most BINs were congruent with traditionally recognized species. Deep intraspecific genetic divergences in some clades highlighted the need for taxonomic revision in several species-complexes and species-groups. Research has yielded the first molecular characterization of nine species, with most having restricted distributions and confirmed the existence of several species which had been declared extinct regionally.

Gut Dysbiosis in Ocular Mucous Membrane Pemphigoid.

Mucous Membrane Pemphigoid is an orphan multi-system autoimmune scarring disease involving mucosal sites, including the ocular surface (OcMMP) and gut. Loss of tolerance to epithelial basement membrane proteins and generation of autoreactive T cell and/or autoantibodies are central to the disease process. The gut microbiome plays a critical role in the development of the immune system. Alteration in the gut microbiome (gut dysbiosis) affects the generation of autoreactive T cells and B cell autoantibody repertoire in several autoimmune conditions. This study examines the relationship between gut microbiome diversity and ocular inflammation in patients with OcMMP by comparing OcMMP gut microbiome profiles with healthy controls. DNA was extracted from faecal samples (49 OcMMP patients, 40 healthy controls), amplified for the V4 region of the 16S rRNA gene and sequenced using Illumina Miseq platform. Sequencing reads were processed using the bioinformatics pipeline available in the mothur v.1.44.1 software. After adjusting for participant factors in the multivariable model (age, gender, BMI, diet, proton pump inhibitor use), OcMMP cohort was found to be associated with lower number of operational taxonomic units (OTUs) and Shannon Diversity Index when compared to healthy controls. Within the OcMMP cohort, the number of OTUs were found to be significantly correlated with both the bulbar conjunctival inflammation score (p=0.03) and the current use of systemic immunotherapy (p=0.02). The linear discriminant analysis effect size scores indicated that Streptococcus and Lachnoclostridium were enriched in OcMMP patients whilst Oxalobacter, Clostridia uncultured genus-level group (UCG) 014, Christensenellaceae R-7 group and butyrate-producing bacteria such as Ruminococcus, Lachnospiraceae, Coprococcus, Roseburia, Oscillospiraceae UCG 003, 005, NK4A214 group were enriched in healthy controls (Log10 LDA score < 2, FDR-adjusted p <0.05). In conclusion, OcMMP patients have gut dysbiosis correlating with bulbar conjunctival inflammation and the use of systemic immunotherapies. This provides a framework for future longitudinal deep phenotyping studies on the role of the gut microbiome in the pathogenesis of OcMMP.

Residual Bacteriome after Chemomechanical Preparation of Root Canals in Primary and Secondary Infections

IntroductionSecondary infections may be linked to the presence of residual microorganisms within dental root canals. The purpose of this study was to investigate the bacterial composition of primary and secondary root canal infections before and after chemomechanical treatment. MethodsSamples were collected before chemomechanical preparation (S1) and before obturation (S2) from 19 subjects (10 primary and 9 secondary infections). DNA was extracted, and the V3/V4 region of the 16S ribosomal RNA gene was amplified using the 347 F/803R primers and paired-end sequenced using the MiSeq (Illumina, San Diego, CA) instrument. ResultsSequencing analysis yielded partial 16S ribosomal RNA gene sequences that were taxonomically classified into 10 phyla and 143 genera. The most prevalent phyla in the S1 and S2 samples were Firmicutes and Bacteroides; however, when comparing between sample groups, Proteobacteria seem to have been enriched in secondary infections. The dominant genera in the primary S1 samples were Bacillus, Streptococcus, and Prevotella, whereas Bacillus, Streptococcus, and Selenomonas dominated the secondary infection S1 samples. Bacillus and Marinilactibacillus were the most dominant genera in the primary and secondary S2 samples. The mean number of operational taxonomic units per sample was 32,656 (±12,124 SD) and 37,113 (±16,994 SD) in the S1 and S2 samples, respectively. Alpha and beta diversities presented the same pattern within samples from both groups. ConclusionsGreat interindividual variations in the bacterial composition of the root canal biofilms were observed. There was no difference in the bacterial composition before and after treatment, although some genera survived and seem to be part of a residual microbiome. Our findings revealed a high diversity of the bacterial communities present in root canal infections after chemomechanical treatment, although the majority of the taxa detected were in low abundance.

Observation of the Gut Microbiota Profile in BALB/c Mice Induced by Plasmodium yoelii 17XL Infection.

Rodent malaria caused by Plasmodium yoelii 17XL (Py 17XL) is an ideal animal model for human malaria studies. Although the gut microbiota plays an important role in the occurrence and development of infectious diseases, the gut microbiota associated with Py 17XL infection remains unclear. In the current study, the gut microbiota composition of infected BALB/c mice was surveyed. Mouse fecal samples were collected at 0, 2, 5 days post-infection (dpi), and the gut microbiota was characterized by 16S rRNA sequencing. Operational taxonomic units (OTUs) were 634 ± 26 on average. Firmicutes and Bacteroidetes were typically predominant in the gut microbiota composition at the phylum level. Compared with the Ctrl, Firmicutes was significantly decreased after infection, while Bacteroidetes was notably increased. The most dominant family was Lactobacillaceae in all samples. The alpha diversity index showed that compared with that of the Ctrl, the observed OTU number was decreased at 2 dpi and then slightly increased at 5 dpi. LEfSe analysis revealed several bacterial taxa were notably related to Py-infected mice at the phylogenetic level. Several bacterial genera, such as Lactobacillus, were overrepresented in the Py-infected fecal microbiota at 2 dpi, while Muribaculaceae was overrepresented at 5 dpi. Moreover, Alistipes and Helicobacter were overrepresented at 5 dpi compared with 2 dpi. The results indicated Py infection could alter the gut microbiota composition of mice. Besides, biomarkers could serve as direct targets to elucidate their roles in the progression and pathogenesis of malaria and provide insights into studies of antimalarial drugs and malaria vaccines.

Effect of rapeseed straw-derived biochar on soil bacterial community structure at tillering stage of Oryza Sativa.

Numerous studies have reported the dynamics of microbes when biochar was applied, whereas the information on the alterations of bacterial community after application of rapeseed straw-derived biochar is limited. A pot experiment with two rapeseed straw-derived biochar application treatments (with biochar application at the rate of 200g/pot, C1, and without biochar application, 0g/pot, C0) was conducted. No significant differences were observed in the number of operational taxonomic units, observed species, Shannon index, Simpson index, Chao1, ACE, and phylogenetic diversity whole tree between the C1 and C0 treatments. Taxonomic analysis at the phylum level showed that the abundances of Bacteroidetes and Parcubacteria were higher in the C1 treatment compared to the C0 treatment, while Acidobacteria, Chloroflexi, Rokubacteria, Berkelbacteria, and Latescibacteria were observed with higher abundance in the C0 treatment compared to the C1 treatment. Taxonomic analysis at the genus level showed that the abundances of Gracilibacter, Lentimicrobium, unidentified Rikenellaceae, Hydrogenophaga, and Bacillus were higher in the C1 treatment compared to the C0 treatment, while Candidatus Solibacter, Candidatus Koribacter, and Lutispora abundances were found to be higher in the C0 treatment compared to the C1 treatment. Obvious clusters were observed between the C1 and C0 treatments in both principal component analysis and nonmetric multidimensional scaling. These results indicate that soil bacterial community was altered after rapeseed straw-derived biochar was applied.

Cropping practices manipulate soil bacterial structure and functions on the Qinghai–Tibet Plateau

There is an increasing awareness of the adverse environmental effects of the intensive practices used in modern crop farming, such as those that cause greenhouse gas emissions and nutrient leaching. Harnessing beneficial microbes by changing planting practices presents a promising strategy for optimizing plant growth and agricultural sustainability. However, the characteristics of soil microorganisms under different planting patterns remain uncertain. We conducted a study of soil bacterial structure and function under monoculture vs. polyculture planting regimes using 16S rRNA gene sequencing on the Qinghai–Tibet Plateau. We observed substantial variations in bacterial richness, diversity, and relative abundances of taxa between gramineous and leguminous monocultures, as well as between gramineae–legume polycultures. The number of operational taxonomic units and alpha and beta diversity were markedly higher in the leguminous monocultures than in the gramineous monocultures; conversely, network analysis revealed that the interactions among the bacterial genera in the gramineous monocultures were more complex than those in the other two planting regimes. Moreover, nitrogen fixation, soil detoxification, and productivity were increased under the gramineous monocultures; more importantly, low soil-borne diseases (e.g., animals parasitic or symbiont) also facilitated strongly suppressive effects toward soil-borne pathogens. Nevertheless, the gramineae–legume polycultures were prone to nitrate seepage contamination, and leguminous monocultures exhibited strong denitrification effects. These results revealed that the gramineous monoculture is a more promising cropping pattern on the Qinghai–Tibetan Plateau. Understanding the bacterial distribution patterns and interactions of crop-sensitive microbes presents a basis for developing microbial management strategies for smart farming.

Effects of Feeding Frequency and Dietary Protein/Carbohydrate Ratios on Gilthead Seabream (Sparus aurata) Intestinal Functionality and Health

The present study evaluated the effects of feeding frequency (FF) and dietary protein/carbohydrate (P/CH) ratios on intestinal histomorphology, microbiota profile, and digestive and oxidative stress-related enzyme activities of gilthead seabream (Sparus aurata). To this purpose, two practical diets were formulated: one with 50% P and 10% CH (P50/CH10) and other with 40% P and 20% CH (P40/CH20). Triplicate groups of fish with9.1±0.01 gwere fed these diets for 60 days until visual satiation at a FF of 1, 2, or 3 meals per day. Distal intestine histomorphology was not affected by diet composition or FF. However, the pyloric caeca (PC) of fish fed 1 meal per day presented more gut fold height alterations than the other groups, except in fish fed diet P50/CH10 3 meals per day, where no changes was observed. Fish fed diet P40/CH20 3 meals per day also presented higher PC submucosa cellularity than the other groups. Fish fed diet P40/CH20 presented a higher number of operational taxonomic units, microbial richness, and diversity indices than fish fed diet P50/CH10. Amylase was the only measured digestive enzyme affected by the experimental conditions, presenting higher activity in fish fed diet P50/CH10 once per day. Glucose-6-phosphate dehydrogenase activity was lower in fish fed 2 meals per day than only 1. While catalase activity was lower in fish fed 2 than 3 meals per day. Glutathione reductase activity was the only measured parameter affected both by dietary P/CH ratio and FF, being inferior in fish fed once per day the P50/CH10 diet than the P40/CH20 diet and, also in the P50/CH10 diet, to fish fed 1 than those fed 3 meals per day. Overall, no major interactions was observed between dietary P/CH ratio and FF; however, a P40/CH20 diet fed 2 meals per day might be recommended for gilthead seabream juveniles.

Effect of Dietary Plant Feedstuffs and Protein/Carbohydrate Ratio on Gilthead Seabream (Sparus aurata) Gut Health and Functionality

This study investigated, for the first time, the integrated effects of dietary protein source and protein/carbohydrate (P/CH) ratio on gilthead seabream gut histomorphology, microbiota composition, digestive enzymes activity, and immunological and oxidative stress-related gene expressions. Four isolipidic diets: two fishmeal-based (FM) and two plant feedstuff (PF)-based diets, with P/CH ratios of 50/10 or 40/20 each (FM-P50/CH10; FM-P40/CH20; PF-P50/CH10; PF-P40/CH20), were tested. PF-based diets lead to more histomorphological alterations than FM-based diets. P/CH ratio had no relevant effect on gut histomorphology. Gut mucosa of fish fed PF-based diets presented a higher number of operational taxonomic units, and richness and diversity indices, while the P/CH ratio did not affect those parameters. The α-amylase activity was lower in fish fed with PF-based diets and in fish fed the P40/CH20 diets. Regarding the immune-related genes, only cyclooxygenase-2 was affected, being higher in fish fed the P50/CH10 diets than the P40/CH20 diets. Fish fed the FM-based diets presented higher expression of glutathione reductase and glutathione peroxidase, while fish fed the P50/CH10 diet had higher expression of superoxide dismutase. In conclusion, PF-based diets can compromise gut absorptive and digestive metabolism, but decreasing the dietary P/CH ratio had little effect on the parameters measured.

Effects of Nutrient Levels and Rice Cultivation on Taxonomic and Functional Diversity of Bacterial Communities in Flooded Soils of the Hanon Maar Crater, Korea

Agricultural land use may deteriorate soil bacterial diversity and function in an agroecosystem. This study aimed to explore the impact of agricultural disturbance on the taxonomic and functional diversity of soil bacteria using a high-throughput sequencing method. We examined the bacterial community diversity in five types of flooded soils in the Hanon Maar Crater from two types of canals characterized by different nutrient levels and three field types with a different rice cultivation history. Proteobacteria (43.2%), Chloroflexi (19.8%), Acidobacteria (15.8%), Actinobacteria (5.1%), and Nitrospirae (5.0%) were the dominant phyla (&gt;5%). The relative abundance of Actinobacteria was 7.1 times greater in the abandoned fields than in the polluted canal. Alpha diversity indices of taxonomic diversity showed strong negative correlations with C, N, and NH4+ levels. The 1.7-fold greater number of operational taxonomic units (OTUs) in abandoned fields than in paddy fields may be caused by factors other than nutrients. Functional analysis revealed that 11 putative functions, including cellulolysis and ligninolysis, were significantly affected by soil management. Functional diversity indices showed negative correlations with electrical conductivity (EC) and NH4+. Nitrogen input had a greater effect on bacterial taxonomic diversity than on functional diversity. Available P was positively correlated with the diversity indices. Taken together, these results suggest that keeping land fallow for more than 5 years and monitoring of C, N, and P levels are practical approaches for restoring taxonomic diversity but not functional diversity of soil bacteria. Our study demonstrated a decoupled response of taxonomic and functional diversity to rice cultivation, highlighting the necessity of further studies on the impact of decoupling on the stability of ecosystem functioning.

Composition, activity and diversity of bacterial and fungal communities responses to inputs of phosphorus fertilizer enriched with beneficial microbes in degraded Brunic Arenosol

AbstractAnthropogenic‐induced deterioration of soil health remains a global problem, resulting in a diminished productivity of agroecosystems. In order to improve soil quality, we investigated the impact of phosphorus biofertilizer on the microbiological parameters of soil (type Brunic Arenosol) degraded as a result of inappropriate cultivation and fertilization, characterized by low pH and decrease in K and Mg content. Two‐year field experiment included control treatment (FC) without microbial enrichment and FA100 (fertilizer amendment at optimal dose) and FA60 (fertilizer amendment at 40% reduced dose) treatments containing beneficial microorganisms. The results showed that the biofertilizer enhanced soil enzymatic activity (as expressed by the increased activities of urease, protease, acid phosphomonoesterase, and β‐glucosidase), increased number of operational taxonomic units associated with metabolic processes (including phosphorus related pathways and degradation of xenobiotics), improved crop yield, increased bacterial diversity, and changed the quantity of phytoavailable phosphorus in the soil. Biofertilizer also stimulated the occurrence of plant growth promoting microorganisms involved in phosphorus biotransformations, decomposition of organic matter, nitrogen fixation, and protection plants against pathogens. Next generation sequencing (NGS) and Biolog analyses showed that the composition of soil microbiome was affected also by soil sampling time, suggesting seasonal variations in the preferred carbon sources and level of C‐substrates utilization, and pointing the differences in the relative abundance of individual microbial groups at particular stages of the experiment. Taking into consideration the improvement of microbiological indicators of soil health, phosphorus biofertilizer seems to be effective approach to implement in sustainable agriculture linking soil microbiome quality with the general soil condition.

Influence of tea-Pleurotus ostreatus intercropping on soil fungal diversity and community structure

Understanding the relationship between soil fungal communities and soil function is vital to establish a sustainable and ecologically friendly tea (Camellia sinensis L.) cultivation. However, there is limited research on the response of soil fungal communities to tea-fungus intercropping, particularly how it is related to soil biodiversity and fertility. Here, we assessed and compared the fungal communities using a metabarcoding technique, soil properties in three plantations (1, 2, and 5 yr of tea-Pleurotus intercropping plantations), and a 5 yr chemically fertilized monoculture plantation. We obtained a total of 3493 operational taxonomic units (OTUs) from four tea plantations. Five hundred and ninety-three fungal OTUs are shared by all plantations, and the other 471 fungal OTUs are shared by three plantations. The largest number of OTUs was recorded in 5 yr tea-Pleurotus intercropped plantations (N = 2040), followed by 2 yr (N = 2024) and then 1 yr (N = 1471), while the chemically fertilized plantation recorded 1823 OTUs. Tea-Pleurotus intercropping showed a significant effect on the increased diversity of soil fungal diversity compared with the monoculture tea cultivations. Fungal groups Basidiomycota, Ascomycota, and Mortierellomycota were the most abundant taxonomic groups recorded in all soil samples. Principal coordinate analysis revealed that fungal community composition in tea-Pleurotus intercropped plantations and monoculture tea plantations was significantly different. Besides, redundancy analysis revealed that soil nutrients significantly influence soil fungal community composition. Our results demonstrate that tea-Pleurotus intercropping may offer long-term benefits to soil biodiversity and sustainable benefits in the tea plantations.

High-Throughput Sequencing-Based Analysis of Rhizosphere and Diazotrophic Bacterial Diversity Among Wild Progenitor and Closely Related Species of Sugarcane (Saccharum spp. Inter-Specific Hybrids).

Considering the significant role of genetic background in plant-microbe interactions and that most crop rhizospheric microbial research was focused on cultivars, understanding the diversity of root-associated microbiomes in wild progenitors and closely related crossable species may help to breed better cultivars. This study is aimed to fill a critical knowledge gap on rhizosphere and diazotroph bacterial diversity in the wild progenitors of sugarcane, the essential sugar and the second largest bioenergy crop globally. Using a high-throughput sequencing (HTS) platform, we studied the rhizosphere and diazotroph bacterial community of Saccharum officinarum L. cv. Badila (BRS), Saccharum barberi (S. barberi) Jesw. cv Pansahi (PRS), Saccharum robustum [S. robustum; (RRS), Saccharum spontaneum (S. spontaneum); SRS], and Saccharum sinense (S. sinense) Roxb. cv Uba (URS) by sequencing their 16S rRNA and nifH genes. HTS results revealed that a total of 6,202 bacteria-specific operational taxonomic units (OTUs) were identified, that were distributed as 107 bacterial groups. Out of that, 31 rhizobacterial families are commonly spread in all five species. With respect to nifH gene, S. barberi and S. spontaneum recorded the highest and lowest number of OTUs, respectively. These results were validated by quantitative PCR analysis of both genes. A total of 1,099 OTUs were identified for diazotrophs with a core microbiome of 9 families distributed among all the sugarcane species. The core microbiomes were spread across 20 genera. The increased microbial diversity in the rhizosphere was mainly due to soil physiochemical properties. Most of the genera of rhizobacteria and diazotrophs showed a positive correlation, and few genera negatively correlated with the soil properties. The results showed that sizeable rhizospheric diversity exists across progenitors and close relatives. Still, incidentally, the rhizosphere microbial abundance of progenitors of modern sugarcane was at the lower end of the spectrum, indicating the prospect of Saccharum species introgression breeding may further improve nutrient use and disease and stress tolerance of commercial sugarcane. The considerable variation for rhizosphere microbiome seen in Saccharum species also provides a knowledge base and an experimental system for studying the evolution of rhizobacteria-host plant association during crop domestication.

Acupuncture improves the symptoms, intestinal microbiota, and inflammation of patients with mild to moderate Crohn's disease: A randomized controlled trial.

SummaryBackgroundThe efficacy and mechanisms of acupuncture for Crohn's disease (CD) are not well understood. We investigated its effects on symptoms, intestinal microbiota, and circulating inflammatory markers in CD patients.MethodsThis 48-week, randomized, sham controlled, parallel-group clinical trial was performed at a tertiary outpatient clinic in China. From April 2015 to November 2019, 66 patients (mean age 40·4, 62·1% were male, all were Han Chinese) with mild to moderate active CD and unresponsive to drug treatment were enrolled and randomly assigned equally to an acupuncture group or a sham group. The treatment group received 3 sessions of acupuncture plus moxibustion per week for 12 weeks and a follow-up of 36 weeks. Clinicaltrials.gov: NCT02559037.FindingsAt week 12, the clinical remission rate (the primary outcome) and clinical response rate of acupuncture group were significantly higher than that of sham group, with a difference of 42·4% (95% CI: 20·1%-64·0%) and 45·5% (95% CI: 24·0%-66·9%), respectively, both of which maintained at week 48. The acupuncture group had significantly lower CD activity index and C-reactive protein level at week 12, which maintained at 36-week follow-up. The CD endoscopic index of severity, histopathological score, and recurrence rate at week 48 were significantly lower in acupuncture group. The number of operational taxonomic unit of intestinal microbiota and relative abundance of Faecalibacterium prausnitzii and Roseburia faecis were increased. Plasma diamine oxidase, lipopolysaccharide, and Th1/Th17 related cytokines were decreased in 12-week after acupuncture.InterpretationAcupuncture was effective in inducing and maintaining remission in patients with active CD, which was associated with increased abundance of intestinal anti-inflammatory bacteria, enhanced intestinal barrier, and regulation of circulating Th1/Th17-related cytokines.FundingNational Key Basic Research Program of China (2015CB554500 and 2009CB522900), Shanghai Rising-Star Program (19QA1408100).

Effects of dietary ARA, DHA, and carbohydrates levels on gilthead sea bream liver and intestine oxidative stress, tissue histomorphology, and gut microbiota

The present study aims evaluate the oxidative status, histomorphology of liver and intestine, and intestinal microbiota modulation of gilthead sea bream juveniles (initial body weight = 47.5 g) fed four isoproteic and isolipidic diets (47% protein; 18% lipids) with high or low gelatinized starch levels (20% or 5%; diets HS or LS, respectively) and different dietary ARA or DHA content (2.3/0.3 or 0/2.6, diets ARA or DHA, respectively).ARA-rich diets reduced liver and intestine lipid peroxidation (LPO) circa 12 and 66%, respectively. Dietary ARA also increased liver glutathione redox status (total, reduced (GSH) and oxidized glutathione (GSSG)) circa of 35% but only in the HS diets. Independently of dietary starch level, dietary ARA also reduced GSSG content (80 and 63 nmol g−1 tissue) and oxidative stress index (OSI) (8.7 and 7%) in the intestine. Fish fed DHA diets had increased hepatic superoxide dismutase (SOD) (749.1 and 489.1 U mg protein−1) and glutathione reductase (GR) (3.7 to 1.9 mU mg protein−1) activities. In the intestine, dietary ARA or DHA did not induce alterations in the activity of the antioxidant enzymes. Dietary starch improved liver OSI (1.5%), increased intestinal GSSG (80 and 128 nmol g−1 tissue), and decreased intestinal LPO values (104 nmol MDA g−1 tissue) in fish fed the DHA diets. Fish fed the HS diets had increased hepatic glucose-6-phosphate dehydrogenase (G6PDH) (171.4 and 166 mU mg protein−1), GR (2 and 3.71 mU mg protein−1), and glutathione peroxidase (GPX, only in DHA diets) (63.8 mU mg protein−1) activities, but decreased GR (27.2 and 27.6 mU mg protein−1) and SOD (2089.7 and 2158.8 U mg protein−1) activities in the intestine.Diet composition did not induce major histomorphological alterations in the distal intestine. Nevertheless, the HS diets, especially when combined with DHA, promoted hepatocyte hypertrophy and alterations in nuclei position.Compared to the DHA diets, in fish fed the ARA diets, mucosa bacterial profile had a reduced number of operational taxonomic units (10.3 and 12.0), richness (0.6 and 0.7), and diversity (2.2 and 2.3), and higher similarity between bacterial communities (85.0 and 80.4%).In conclusion, fish fed high dietary ARA presented lower hepatic and intestinal LPO and fewer hepatocyte morphological alterations than fish fed high DHA diets. Furthermore, interactive effects between dietary starch and DHA on liver and intestine GSH metabolism, antioxidant enzymes, LPO susceptibility, and liver histomorphology may be attenuated by a balanced ARA/DHA dietary ratio.

Effects of Replacing Fish Meal with Distillers’ Dried Grains with Solubles on the Growth Performance and Gut Microbiota in Juvenile Pacific Whiteleg Shrimp Litopenaeus vannamei

AbstractThis research was conducted to assess the effects of replacing fish meal (FM) with distillers’ dried grains with solubles (DDGS) at various levels (D1 [0% of total diet] as control diet, D2 [2%], D3 [4%], D4 [6%], D5 [8%], D6 [12%], and D7 [16%]) on the growth performance and gut microbiota in juvenile Pacific whiteleg shrimp Litopenaeus vannamei. Shrimp with an initial weight of 0.23 ± 0.00 g (mean ± SD) were stocked (40 shrimp/tank) in seven different tanks, with three replicates of each treatment group. Shrimp were fed their respective experimental diets for 56 d. Afterwards, an Illumina‐based sequencing method was used to examine the intestinal bacterial composition of the shrimp. The results showed an enhancement of growth performance, including final weight and weight gain, in shrimp that were fed DDGS diets. In addition, the feed conversion ratio was significantly lower in shrimp that were fed D6 and D8 than in shrimp that received D0. Survival rates ranged from 76.6% to 92.50%. The richness estimates (Chao 1 and the abundance‐based coverage estimator) and diversity indices (Shannon and Simpson) of the microbial community were affected when DDGS were included in the shrimp diet. Beneficial bacteria, including Proteobacteria, Bacteroidetes, and Actinobacteria, dominated the gut microbiota at the phylum level for shrimp that were fed DDGS diets. The number of operational taxonomic units obtained ranged from 783 to 920. These results suggest that replacing FM with DDGS at 8% (D5) in the total shrimp diet could enhance the growth performance and affect gut microbiota composition in Pacific whiteleg shrimp.

Positive effect of filtration additives for increasing environmental DNA detections in summer and winter oceanic waters

AbstractEnvironmental DNA (eDNA) is a convenient biodiversity monitoring tool, and many studies have focused on river and coastal areas, while deep‐water oceanic surveys are rare. However, using eDNA techniques to learn about oceanic communities may also be a useful approach. We tested methods to enhance ocean eDNA collections adding four different materials (sediment, diatomite, zirconia bead, and molecular sieve) in combination with 0.45‐μm pore size filter, also compared 0.22‐μm pore size filter, using five 2‐L volume replicates. The experiments were conducted off the Pacific coast of Hokkaido, Japan, in summer and winter. The winter trial also included a larger water volume (10 L, duplicate) experimental treatment. The added diatomite showed the highest number of detected operational taxonomic units (OTU) in the summer trial, while sediment and beads showed higher numbers in winter. GLM analysis showed that pore size does not affect the number of OTUs, while season and the other four additive materials were significant effects. The added materials in the water likely trapped more eDNA and prevented it from passing through the filters. The 10‐L filtered sample had more OTUs than combining five replicates of 2‐L filtered samples. Comparison among the same trial revealed that DNA composition in the water is variable, and detected species differed even in the same water sample. Species richness and diversity were higher in winter than in summer, and species compositions differed between seasons. The greater numbers of species detected using filtration additives suggest these methods could be useful for eDNA ocean biodiversity surveys.

Effects of ultramafic topsoil stockpiling during mine activities on its microbial diversity and other microbiological and physicochemical characteristics

Nowadays, ecological restoration is considered the best solution for the rehabilitation of mining-degraded areas, particularly when it concerns valuable ecosystems. This is the case in New Caledonia, a hot spot of biodiversity, with 82% of endemic plant species in ultramafic soils. The use of topsoil to restore mined areas is an important practice. However, topsoil stockpiling can reduce soil fertility. We studied the evolution of different properties of two topsoils stored in 10 m height piles on mined areas, in order to characterize possible degradations. The effects of storage duration, depth, and topsoil origin were analyzed, focusing mainly on bacterial and fungal diversity assessed after bar-coded pyrosequencing, and expressed by operational taxonomic units (OTU). Microbial activity (carbon dioxyde production), arbuscular mycorrhizal fungi (AMF) spore numbers, bulk density and different other physicochemical characteristics were also determined. The studied ultramafic soils were characterized by a relatively high microbial diversity with 45 bacterial phyla and 7 fungal phyla. Bacterial and fungal OTU numbers did not vary significantly after 12 months of storage, but the community structures of these groups were changed. AMF diversity was significantly reduced by the storage. Microbial activity, AMF spore numbers, soil organic carbon, total nitrogen, cation exchange capacity, and carbon to nitrogen ratio (C/N) decreased significantly starting from 3 to 9 months of topsoil storage. In contrast, soil bulk density and pH increased, and extractable concentrations of potentially toxic metals varied only slightly. All the changes induced by topsoil stockpiling in microbial population structure, AMF diversity, and other biotic and abiotic traits may negatively affect soil functions and create perturbations of the reconstructed ecosystems after revegetation. It is then necessary to reduce the storage of ultramafic topsoils as far as possible. In all cases, the stockpiling should not exceed six months before its use in ecosystem restoration. It is also recommended to reduce the height of the stockpiles, when possible, to 1 m or less to minimize the compaction and the anaerobiosis.

Metabarcoding of the phytotelmata of Pseudalcantarea grandis (Bromeliaceae) from an arid zone.

BackgroundPseudalcantarea grandis (Schltdl.) Pinzón & Barfuss is a tank bromeliad that grows on cliffs in the southernmost portion of the Chihuahuan desert. Phytotelmata are water bodies formed by plants that function as micro-ecosystems where bacteria, algae, protists, insects, fungi, and some vertebrates can develop. We hypothesized that the bacterial diversity contained in the phytotelma formed in a bromeliad from an arid zone would differ in sites with and without surrounding vegetation. Our study aimed to characterize the bacterial composition and putative metabolic functions in P. grandis phytotelmata collected in vegetated and non-vegetated sites.MethodsWater from 10 individuals was sampled. Five individuals had abundant surrounding vegetation, and five had little or no vegetation. We extracted DNA and amplified seven hypervariable regions of the 16S gene (V2, V4, V8, V3–6, 7–9). Metabarcoding sequencing was performed on the Ion Torrent PGM platform. Taxonomic identity was assigned by the binning reads and coverage between hit and query from the reference database of at least 90%. Putative metabolic functions of the bacterial families were assigned mainly using the FAPROTAX database. The dominance patterns in each site were visualized with rank/abundance curves using the number of Operational Taxonomic Units (OTUs) per family. A percentage similarity analysis (SIMPER) was used to estimate dissimilarity between the sites. Relationships among bacterial families (identified by the dominance analysis and SIMPER), sites, and their respective putative functions were analyzed with shade plots.ResultsA total of 1.5 million useful bacterial sequences were obtained. Sequences were clustered into OTUs, and taxonomic assignment was conducted using BLAST in the Greengenes databases. Bacterial diversity was 23 phyla, 52 classes, 98 orders, 218 families, and 297 genera. Proteobacteria (37%), Actinobacteria (19%), and Firmicutes (15%) comprised the highest percentage (71%). There was a 68.3% similarity between the two sites at family level, with 149 families shared. Aerobic chemoheterotrophy and fermentation were the main metabolic functions in both sites, followed by ureolysis, nitrate reduction, aromatic compound degradation, and nitrogen fixation. The dominant bacteria shared most of the metabolic functions between sites. Some functions were recorded for one site only and were related to families with the lowest OTUs richness. Bacterial diversity in the P. grandis tanks included dominant phyla and families present at low percentage that could be considered part of a rare biosphere. A rare biosphere can form genetic reservoirs, the local abundance of which depends on external abiotic and biotic factors, while their interactions could favor micro-ecosystem resilience and resistance.

Black soldier fly meal effects on meagre health condition: gut morphology, gut microbiota and humoral immune response

The effects of black soldier fly (Hermetia illucens) meal (HM) on gut morphology, gut microbial community, and humoral immune response was evaluated in meagre (Argyrosomus regius) juveniles. For that purpose, fish with 18.0±0.02 g were fed a control diet (CTR) without HM, and 3 other diets including 10, 20 and 30% HM (diets HM10, HM20 and HM30, respectively), replacing 17, 35 and 52% of fish meal (FM), for 9 weeks. The meagre distal intestine (DI) showed no significant histomorphologic alterations in fold height, lamina propria, submucosa width and cellularity, and enterocytes shape, between dietary treatments. Increasing numbers of eosinophilic granulocytes and intraepithelial leukocytes were observed in fish fed the HM30 diet compared to the CTR and HM10 diets. The mean DI score was higher in meagre fed the HM30 diet, denoting increased overall histomorphological alterations in that group compared to fish fed the CTR diet. No differences in gut bacterial profiles (number of operational taxonomic units, microbiota richness, diversity, and similarity indices) were observed between dietary treatments, either in allochthonous (digesta) and autochthonous (mucosa) communities. Plasma anti-protease activity increased with increasing dietary HM level, while no significant differences were observed in the plasmatic protease, peroxidase, lysozyme and bactericidal activities, nitric oxide production and total immunoglobulins. Overall, and in order to avoid gut histomorphological alterations, an inclusion level up to 10% of HM, corresponding to 17% of FM replacement, is recommended for meagre juveniles.