Number Of Operational Taxonomic Units Research Articles

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 (>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.

Trophic and symbiotic links between obligate-glacier water bears (Tardigrada) and cryoconite microorganisms

Insights into biodiversity and trophic webs are important for understanding ecosystem functions. Although the surfaces of glaciers are one of the most productive and biologically diverse parts of the cryosphere, the links between top consumers, their diet and microbial communities are poorly understood. In this study, for the first time we investigated the relationships between bacteria, fungi and other microeukaryotes as they relate to tardigrades, microscopic metazoans that are top consumers in cryoconite, a biologically rich and productive biogenic sediment found on glacier surfaces. Using metabarcoding (16S rDNA for bacteria, ITS1 for fungi, and 18S rDNA for other microeukaryotes), we analyzed the microbial community structures of cryoconite and compared them with the community found in both fully fed and starved tardigrades. The community structure of each microbial group (bacteria, fungi, microeukaryotes) were similar within each host group (cryoconite, fully fed tardigrades and starved tardigrades), and differed significantly between groups, as indicated by redundancy analyses. The relative number of operational taxonomic units (ZOTUs, OTUs) and the Shannon index differed significantly between cryoconite and tardigrades. Species indicator analysis highlighted a group of microbial taxa typical of both fully fed and starved tardigrades (potential commensals), like the bacteria of the genera Staphylococcus and Stenotrophomonas, as well as a group of taxa typical of both cryoconite and fully fed tardigrades (likely part of the tardigrade diet; bacteria Flavobacterium sp., fungi Preussia sp., algae Trebouxiophyceae sp.). Tardigrades are consumers of bacteria, fungi and other microeukaryotes in cryoconite and, being hosts for diverse microbes, their presence can enrich the microbiome of glaciers.

Seasonal variation significantly affected bacterioplankton and eukaryoplankton community composition in Xijiang River, China.

Both bacterioplankton and eukaryoplankton communities play important roles in the geochemical cycles and energy flows of river ecosystems. However, whether a seasonal change in bacterioplankton and eukaryoplankton communities is synchronous remains unclear. To test the synchronicity and analyze how physical and chemical environmental factors affect these communities, we compared bacterioplankton and eukaryoplankton communities in surface water samples between March (dry season) and June (rainfall season) considering water environmental factors. Our results showed that there was no significant difference in operational taxonomic unit number, Shannon index, and Chao1 index in bacterioplankton and eukaryoplankton communities between March and June. However, principal component analysis showed that the communities were significantly different between the sampling times and sampling sites. Water temperature (WT), oxidation-reductionpotential (ORP), water transparency (SD), NO3-N, and NH3 significantly influenced bacterioplankton communities, and WT, SD, ORP, and NH4-N significantly influenced eukaryoplankton communities in the river. These results implied that compared with the sampling sites, sampling times more significantly affected the bacterioplankton and eukaryoplankton river communities by influencing WT, ORP, SD, and nitrogen forms.

Diversity of Candidatus Patescibacteria in Activated Sludge Revealed by a Size-‍Fractionation Approach.

Uncultivated members of Candidatus Patescibacteria are commonly found in activated sludge treating sewage and are widely distributed in wastewater treatment plants in different regions and countries. However, the phylogenetic diversity of Ca. Patescibacteria is difficult to examine because of their low relative abundance in the environment. Since Ca. Patescibacteria members have small cell sizes, we herein collected small microorganisms from activated sludge using a filtration-based size-fractionation approach (i.e., 0.45–0.22‍ ‍μm and 0.22–0.1‍ ‍μm fractions). Fractionated samples were characterized using 16S rRNA gene amplicon and shotgun metagenomic sequence ana­lyses. The amplicon ana­lysis revealed that the relative abundance of Ca. Patescibacteria increased to 73.5% and 52.5% in the 0.45–0.22‍ ‍μm and 0.22–0.1‍ ‍μm fraction samples, respectively, from 5.8% in the unfractionated sample. The members recovered from the two size-fractionated samples included Ca. Saccharimonadia, Ca. Gracilibacteria, Ca. Paceibacteria, Ca. Microgenomatia, class-level uncultured lineage ABY1, Ca. Berkelbacteria, WS6 (Ca. Dojkabacteria), and WWE3, with Ca. Saccharimonadia being predominant in both fraction samples. The number of operational taxonomic units belonging to Ca. Patescibacteria was approximately 6-fold higher in the size-fractionated samples than in the unfractionated sample. The shotgun metagenomic ana­lysis of the 0.45–0.22‍ ‍μm fractioned sample enabled the reconstruction of 24 high-quality patescibacterial bins. The bins obtained were classified into diverse clades at the family and genus levels, some of which were rarely detected in previous activated sludge studies. Collectively, the present results suggest that the overall diversity of Ca. Patescibacteria inhabiting activated sludge is higher than previously expected.

Spatial distribution of bacterioplankton community composition and their diversity in Lake Fuxian during thermal stratification period

水体垂向分层是深水湖泊一个重要的特征，这不仅影响水体理化环境因子，而且影响水生生物组成的垂向分布，但是对不同水层水体细菌的多样性和群落结构组成的形成与维持机制知之甚少. 本研究以抚仙湖为研究对象，在水体热力分层期间采集不同位点、不同水层水样，借助16S rDNA Illumina Miseq高通量测序技术，探究水体细菌多样性和群落结构组成的空间分布特征及关键影响因子. 研究结果表明：(1)抚仙湖北部湖心在水深15~40 m处出现温跃层，温度由23℃降至15℃，其余理化环境因子也存在明显的垂向分层现象；与垂向差异相比，表层水体各理化因子在水平方向上的差异相对较小. (2)在水平方向上，南部湖心表层水体细菌alpha多样性(Operational Taxonomic Unit数目和Faith's phylogenetic diversity)最高；在垂向上，水体细菌alpha多样性随着采样水深的增加呈现单峰分布，在30和40 m水层最高；水体细菌alpha和beta多样性的垂向差异均显著大于水平方向差异. (3)表层水体细菌主要由Actinomycetales、unidentified Cyanobacteria、Burkholderiales和Sphingobacteriales组成；温跃层中以Pseudomonadales为主；均温层的优势菌群为unidentified Chloroflexi、Actinomycetales和Burkholderiales. 典范对应分析表明溶解性有机碳、溶解氧、硝态氮、氨氮和总磷浓度是影响细菌群落组成的主要环境因子.;Deep lakes are typically characterized by thermal stratification throughout the year, except for a short mixing period in winter. This vertical partitioning has important effects on many biotic, physical and chemical characteristics of the water column. However, at present, little is known about how these changes affect the vertical distribution of bacterioplankton community diversity. In this study, Lake Fuxian with a relatively long thermal stratification period every year, was chosen for the investigation of bacterioplankton distribution, diversity and composition on August 25th, 2013. 16S rDNA Illumina Miseq high-throughput sequencing technology was performed on DNA extracted from water samples collected from different locations and different water depths. The results showed that: (1) A thermocline appeared in the lake center and in the northern part of this lake at the depth of 15-40 m, with the temperature dropping from 23℃ to 15℃. Other physical and chemical factors also showed obvious vertical stratification pattern. Horizontally, there is no significant difference in physicochemical features. (2) In the horizontal direction, the alpha diversities of plankton bacteria (the number of Operational Taxonomic Units and Faith's phylogenetic diversity) in the surface water of the southern lake center was the highest; in the vertical direction, the alpha diversity gradually increased with the increase of the sampling depth, topping at the depths of 30 m or 40 m, and then gradually decreased; the difference of the bacterioplankton alpha and beta diversity in the vertical direction was significantly greater than those in the horizontal direction. (3) The bacterioplankton in the epilimnion were mainly composed of Actinomycetales, unidentified Cyanobacteria, Burkholderiales and Sphingobacteriales; the relative abundance of Pseudomonadales in the thermocline significantly increased and became dominant; unidentified Chloroflexi, Actinomycetales and Burkholderiales were the dominant bacterial taxa in the hypolimnion. The canonical correspondence analysis demonstrated that the concentrations of dissolved organic carbon, dissolved oxygen, nitrate, ammonium and total phosphorus are the significant environmental variables shaping the bacterial community's composition and diversity.

Distribution Characteristics and Species Diversity of Bacteria in Hepatocellular Carcinoma Tissues

This study was to explore the differences in the distribution and species diversity of bacteria between hepatocellular carcinoma (HCC) tissues and normal liver tissues. 28 HCC patients treated with surgery were selected as the research objects (HCC group), and 19 healthy volunteers with normal physical examinations were included in the control group (Normal group). The tumor specimens were obtained by intraoperative and biopsy puncture, and a 16S ribosomal ribonucleic acid (rRNA) library was constructed. Based on the sequencing data obtained by the IlluminaHi Seq sequencing platform, the differences of bacteria in the liver tissues of the HCC group and the Normal group were analyzed at the level of phyla, family, and genus. The Ace, Chao1, and Shannon of the two groups were compared. The results showed that IlluminaHi Seq sequencing obtained a total of 11,714,659 valid sequences, with an average of 131,625 sequences per sample. The proportions of Bacteroidetes, Firmicutes, and Proteobacteria in HCC group and Normal group were 48.75% versus 34.16%, 37.44% versus 18.02%, and 10.85% versus 39.26%, respectively. The Bacteroidaceae, Prevotellaceae, Lachnospiraceae, and Ruminococcaceae accounted for 22.49%, 20.62%, 16.54%, and 19.93% in Normal group; while those in the HCC tissues accounted for 26.83%, 14.22%, 11.14%, and 13.18%, respectively. The dominant bacteria at the genus level in HCC group and Normal group were Bacteroides and Prevotella-9, with the proportions of 24.19% versus 26.04% and 14.19% versus 8.44%, respectively. The difference in operational taxonomic unit (OTU) numbers of HCC and Normal group were compared and analyzed, which were 1,266 and 1,082, respectively, and the number of common OTU in the two tissues was 875. The Ace in HCC tissue and normal liver tissue were 1063.8±66.79 and 1003.6±52.19, respectively. The Ace in HCC tissue was greater than that in normal liver tissue (P < 0.05). The Chao1 and Shannon in HCC tissue were 1022.9±67.74 and 5.4269±0.3608, respectively; while those in normal liver tissue were 1003.6±66.79 and 5.2842±0.9714, respectively. The Chao1 and Shannon in HCC tissues were much higher than those in Normal group (P < 0.05). It showed that there was no difference in the types of bacterial species in HCC tissues, but the proportions of their flora at the level of phyla, family, and genus changed greatly, which may be related to the occurrence of HCC. This study could provide a reference for the diagnosis and treatment of HCC.

Fecal microbiota in inflammatory bowel disease: Studies of lactobacillus and bifidobacteria diversity

<br><b>Background:</b> Diversity of microbial species is a hallmark of dysbiosis in inflammatory bowel disease (IBD). This study was undertaken to determine whether the diversity of lactobacilli and bifidobacteria, two regulatory microbial genera, is altered in patients with IBD. <b>Methods:</b> DNA from fecal samples of 20 healthy volunteers, 20 patients with ulcerative colitis (UC), and 25 patients with Crohn's disease (CD) was amplified by the polymerase chain reaction (PCR) for 16S ribosomal RNA gene sequences specific to genus Lactobacillus and Bifidobacterium. Real-time PCR was done to quantitate bacterial abundance. Amplified DNA was also bar coded and sequenced on the Roche 454 platform. Individual operational taxonomic units (OTUs) were taken as sequences with at least 97% similarity. <b>Results:</b> Abundance of Lactobacillus was significantly increased in UC compared to controls; no other difference in Lactobacillus or Bifidobacterium abundance was found between the three groups. Median reads for genus Lactobacillus was similar between control (940), UC (994), and CD (960) groups. The median number of OTUs per sample was not significantly different between controls (6), UC (5.5) and CD (7). The Shannon index of community diversity was similar between controls (median 1.12), UC (median 1.13) and CD (median 1.11). The Simpson D index was also similar between controls (median 0.393), UC (median 0.439) and CD (median 0.409). Median reads for genus Bifidobacterium was similar between control (846), UC (1052), and CD (964) groups. The median number of Bifidobacteria OTUs per sample was similar for controls (6), UC (7) and CD (8.5). The Shannon index of community diversity was similar between controls (median 0.75), UC (median 1.0) and CD (median 1.14). The Simpson D index was also similar between controls (median 0.570), UC (median 0.422) and CD (median 0.409). <b>Conclusion:</b> The abundance of Lactobacillus was increased in UC. Diversity of genus Lactobacillus and Bifidobacterium was not altered in either UC or CD.<br>