Feed Types Driven Differentiation of Microbial Community and Functionality in Marine Integrated Multitrophic Aquaculture System

Integrated multi trophic aquaculture (IMTA) improves the production of aquatic animals by promoting nutrient utilization through different tropical levels. Microorganisms play an important role in elements cycling, energy flow and farmed-species health. The aim of this study was to evaluate how feed types, fresh frozen fish diet (FFD) or formulated diet (FD), influence the microbial community diversity and functionality in both water and sediment in a marine IMTA system. Preferable water quality, higher animal yields and higher cost efficiency were achieved in the FD pond. Feed types changed the pond bacterial community distribution, especially in the rearing water. The FFD pond was dominated with Cyanobacteria in the water, which played an important role in nitrogen fixation through photosynthesis due to the high nitrogen input of the frozen fish diet. The high carbohydrate composition in the formulated diet triggered higher metabolic pathways related to carbon and lipid metabolism in the water of the FD pond. Sediment had significantly higher microbial diversity than the rearing water. In sediment, the dominating genus, Sulfurovum and Desulfobulbus, were found to be positively correlated by network analysis, which had similar functionality in sulfur transformation. The relatively higher rates of antibiotic biosynthesis in the FFD sediment might be related to the pathogenic bacteria introduced by the trash fish diet. The difference in microbial community composition and metabolic pathways may be associated with the different pathways for nutrient cycling and animal growth performance. The formulated diet was determined to be more ecologically and economically sustainable than the frozen fish diet for marine IMTA pond systems.

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Spatial and Annual Variation in Microbial Abundance, Community Composition, and Diversity Associated With Alpine Surface Snow

Frontiers in Microbiology ◽

10.3389/fmicb.2021.781904 ◽

2021 ◽

Vol 12 ◽

Author(s):

Lucas Fillinger ◽

Kerstin Hürkamp ◽

Christine Stumpp ◽

Nina Weber ◽

Dominik Forster ◽

...

Keyword(s):

Climate Change ◽

Microbial Community ◽

Community Composition ◽

Microbial Community Composition ◽

Alpha Diversity ◽

Community Diversity ◽

Taxon Richness ◽

European Alps ◽

Prokaryotic Cell ◽

Surface Snow

Understanding microbial community dynamics in the alpine cryosphere is an important step toward assessing climate change impacts on these fragile ecosystems and meltwater-fed environments downstream. In this study, we analyzed microbial community composition, variation in community alpha and beta diversity, and the number of prokaryotic cells and virus-like particles (VLP) in seasonal snowpack from two consecutive years at three high altitude mountain summits along a longitudinal transect across the European Alps. Numbers of prokaryotic cells and VLP both ranged around 104 and 105 per mL of snow meltwater on average, with variation generally within one order of magnitude between sites and years. VLP-to-prokaryotic cell ratios spanned two orders of magnitude, with median values close to 1, and little variation between sites and years in the majority of cases. Estimates of microbial community alpha diversity inferred from Hill numbers revealed low contributions of common and abundant microbial taxa to the total taxon richness, and thus low community evenness. Similar to prokaryotic cell and VLP numbers, differences in alpha diversity between years and sites were generally relatively modest. In contrast, community composition displayed strong variation between sites and especially between years. Analyses of taxonomic and phylogenetic community composition showed that differences between sites within years were mainly characterized by changes in abundances of microbial taxa from similar phylogenetic clades, whereas shifts between years were due to significant phylogenetic turnover. Our findings on the spatiotemporal dynamics and magnitude of variation of microbial abundances, community diversity, and composition in surface snow may help define baseline levels to assess future impacts of climate change on the alpine cryosphere.

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Seasonal Dynamics and Persistency of Endophyte Communities in Kalidium schrenkianum Shifts Under Radiation Stress

Frontiers in Microbiology ◽

10.3389/fmicb.2021.778327 ◽

2021 ◽

Vol 12 ◽

Author(s):

Jing Zhu ◽

Xiang Sun ◽

Qi-Yong Tang ◽

Zhi-Dong Zhang

Keyword(s):

Microbial Community ◽

Community Composition ◽

Bacterial Communities ◽

Community Dynamics ◽

Microbial Community Composition ◽

Northwest China ◽

Community Diversity ◽

Radiation Stress ◽

Core Microbiome ◽

Essential Components

Endophytes are essential components of plant microbiota. Studies have shown that environmental factors and seasonal alternation can change the microbial community composition of plants. However, most studies have mainly emphasized the transitive endophyte communities and seasonal alternation but paid less attention to their persistence through multiple seasons. Kalidium schrenkianum is a perennial halophyte growing in an arid habitat with radiation stress (137Cs) in northwest China. In this study, K. schrenkianum growing under different environmental stresses were selected to investigate the dynamics and persistency of endophytic microbial communities amid seasons in a year. The results showed that Gammaproteobacteria and unassigned Actinobacteria were the most dominant bacterial communities, while the most dominant fungal communities were Dothideomycetes, unassigned Fungi, and Sodariomycetes. The bacterial community diversity in roots was higher than that in aerial tissues, and root communities had higher diversity in summer and autumn. In contrast, the fungal community diversity was higher in aerial tissues comparing to roots, and the highest diversity was in spring. Season was a determinant factor in the microbial community composition in the roots but not in the aerial tissues. RaupCrick index suggested that the bacterial communities were mainly shaped by stochastic processes. Our research investigated the community traits and members with temporal persistency. For example, bacterial taxa Afipia, Delftia, Stenotrophomonas, Xanthomonadaceae_B_OTU_211, and fungal taxa Neocamarosporium F_OTU_388, F_OTU_404, F_OTU_445, and unassigned Fungi F_OTU_704, F_OTU_767 showed higher frequencies than predicted in all the four seasons tested with neutral community model. The networks of co-occurrence associations presented in two or more seasons were visualized which suggested potential time-continuous core modules in most communities. In addition, the community dynamics and persistency also showed different patterns by radiation levels. Our findings would enhance our understanding of the microbial community assembly under environmental stress, and be promising to improve the development of integrated concept of core microbiome in future.

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Bio-fertilizer Affects Structural Dynamics, Function, and Network Patterns of the Sugarcane Rhizospheric Microbiota

Microbial Ecology ◽

10.1007/s00248-021-01932-3 ◽

2021 ◽

Author(s):

Qiang Liu ◽

Ziqin Pang ◽

Zuli Yang ◽

Fallah Nyumah ◽

Chaohua Hu ◽

...

Keyword(s):

Microbial Community ◽

Community Composition ◽

Pathogenic Bacteria ◽

Bacterial Community Composition ◽

Microbial Community Composition ◽

Fertilizer Efficiency ◽

Size Analysis ◽

Support Vector ◽

Linear Discriminant ◽

Network Patterns

AbstractFertilizers and microbial communities that determine fertilizer efficiency are key to sustainable agricultural development. Sugarcane is an important sugar cash crop in China, and using bio-fertilizers is important for the sustainable development of China’s sugar industry. However, information on the effects of bio-fertilizers on sugarcane soil microbiota has rarely been studied. In this study, the effects of bio-fertilizer application on rhizosphere soil physicochemical indicators, microbial community composition, function, and network patterns of sugarcane were discussed using a high-throughput sequencing approach. The experimental design is as follows: CK: urea application (57 kg/ha), CF: compound fertilizer (450 kg/ha), BF1: bio-fertilizer (1500 kg/ha of bio-fertilizer + 57 kg/ha of urea), and BF2: bio-fertilizer (2250 kg/ha of bio-fertilizer + 57 kg/ha of urea). The results showed that the bio-fertilizer was effective in increasing sugarcane yield by 3–12% compared to the CF treatment group, while reducing soil acidification, changing the diversity of fungi and bacteria, and greatly altering the composition and structure of the inter-root microbial community. Variance partitioning canonical correspondence (VPA) analysis showed that soil physicochemical variables explained 80.09% and 73.31% of the variation in bacteria and fungi, respectively. Redundancy analysis and correlation heatmap showed that soil pH, total nitrogen, and available potassium were the main factors influencing bacterial community composition, while total soil phosphorus, available phosphorus, pH, and available nitrogen were the main drivers of fungal communities. Volcano plots showed that using bio-fertilizers contributed to the accumulation of more beneficial bacteria in the sugarcane rhizosphere level and the decline of pathogenic bacteria (e.g., Leifsonia), which may slow down or suppress the occurrence of diseases. Linear discriminant analysis (LDA) and effect size analysis (LEfSe) searched for biomarkers under different fertilizer treatments. Meanwhile, support vector machine (SVM) assessed the importance of the microbial genera contributing to the variability between fertilizers, of interest were the bacteria Anaerolineace, Vulgatibacter, and Paenibacillus and the fungi Cochliobolus, Sordariales, and Dothideomycetes between CF and BF2, compared to the other genera contributing to the variability. Network analysis (co-occurrence network) showed that the network structure of bio-fertilizers was closer to the network characteristics of healthy soils, indicating that bio-fertilizers can improve soil health to some extent, and therefore if bio-fertilizers can be used as an alternative to chemical fertilizers in the future alternative, it is important to achieve green soil development and improve the climate.

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Host genotype explains rhizospheric microbial community composition: the case of wild cotton metapopulations (Gossypium hirsutum L.) in Mexico

FEMS Microbiology Ecology ◽

10.1093/femsec/fiaa109 ◽

2020 ◽

Vol 96 (8) ◽

Author(s):

Alejandra Hernández-Terán ◽

Marcelo Navarro-Díaz ◽

Mariana Benítez ◽

Rafael Lira ◽

Ana Wegier ◽

...

Keyword(s):

Genetic Variation ◽

Microbial Community ◽

Microbial Communities ◽

Microbial Community Composition ◽

Community Diversity ◽

Rrna Gene ◽

Host Genotype ◽

Plant Host ◽

Wild Cotton

ABSTRACT The rhizosphere provides several benefits to the plant host being a strong determinant for its health, growth and productivity. Nonetheless, the factors behind the assembly of the microbial communities associated with the rhizosphere such as the role of plant genotypes are not completely understood. In this study, we tested the role that intraspecific genetic variation has in rhizospheric microbial community assemblages, using genetically distinct wild cotton populations as a model of study. We followed a common garden experiment including five wild cotton populations, controlling for plant genotypes, environmental conditions and soil microbial community inoculum, to test for microbial differences associated with genetic variation of the plant hosts. Microbial communities of the treatments were characterized by culture-independent 16S rRNA gene amplicon sequencing with Illumina MiSeq platform. We analyzed microbial community diversity (alpha and beta), and diversity structure of such communities, determined by co-occurrence networks. Results show that different plant genotypes select for different and specific microbial communities from a common inoculum. Although we found common amplicon sequence variants (ASVs) to all plant populations (235), we also found unique ASVs for different populations that could be related to potential functional role of such ASVs in the rhizosphere.

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Maize/peanut intercropping improves nutrient uptake of side-row maize and system microbial community diversity

BMC Microbiology ◽

10.1186/s12866-021-02425-6 ◽

2022 ◽

Vol 22 (1) ◽

Author(s):

Xinhua Zhao ◽

Qiqi Dong ◽

Yi Han ◽

Kezhao Zhang ◽

Xiaolong Shi ◽

...

Keyword(s):

Microbial Community ◽

Nutrient Uptake ◽

Peroxidase Activity ◽

Rhizosphere Soil ◽

Microbial Community Composition ◽

Pathogenic Fungi ◽

Nutrient Content ◽

Scientific Basis ◽

Community Diversity ◽

Land Use Efficiency

Abstract Background Intercropping, a diversified planting pattern, increases land use efficiency and farmland ecological diversity. We explored the changes in soil physicochemical properties, nutrient uptake and utilization, and microbial community composition in wide-strip intercropping of maize and peanut. Results The results from three treatments, sole maize, sole peanut and intercropping of maize and peanut, showed that intercropped maize had a marginal advantage and that the nutrient content of roots, stems and grains in side-row maize was better than that in the middle row of intercropped maize and sole maize. The yield of intercropped maize was higher than that of sole cropping. The interaction between crops significantly increased soil peroxidase activity, and significantly decreased protease and dehydrogenase activities in intercropped maize and intercropped peanut. The diversity and richness of bacteria and fungi decreased in intercropped maize rhizosphere soil, whereas the richness of fungi increased intercropped peanut. RB41, Candidatus-udaeobacter, Stropharia, Fusarium and Penicillium were positively correlated with soil peroxidase activity, and negatively correlated with soil protease and dehydrogenase activities. In addition, intercropping enriched the functional diversity of the bacterial community and reduced pathogenic fungi. Conclusion Intercropping changed the composition and diversity of the bacterial and fungal communities in rhizosphere soil, enriched beneficial microbes, increased the nitrogen content of intercropped maize and provided a scientific basis for promoting intercropping in northeastern China.

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Population structure and microbial community diversity of two common tetillid sponges in a tropical reef lagoon

PeerJ ◽

10.7717/peerj.9017 ◽

2020 ◽

Vol 8 ◽

pp. e9017 ◽

Cited By ~ 1

Author(s):

Jake Ivan P. Baquiran ◽

Michael Angelou L. Nada ◽

Niño Posadas ◽

Dana P. Manogan ◽

Patrick C. Cabaitan ◽

...

Keyword(s):

Population Structure ◽

Microbial Community ◽

Global Climate ◽

Microbial Community Composition ◽

Average Density ◽

Community Diversity ◽

Reef Lagoon ◽

Lack Of Information ◽

Tropical Reef ◽

Ecological Success

Sponges are predicted to dominate future reef ecosystems influenced by anthropogenic stressors and global climate change. The ecological success of sponges is attributed to their complex physiology, which is in part due to the diversity of their associated prokaryotic microbiome. However, the lack of information on the microbial community of many sponge species makes it difficult to gauge their interactions and functional contributions to the ecosystem. Here, we investigated the population dynamics and microbial community composition of two tetillid sponges identified as Cinachyrella sp. and Paratetilla sp., which are common on coral bommies in a reef lagoon in Bolinao, northwestern Philippines. The sponges ranged in size from 2.75 ± 2.11 to 6.33 ± 3.98 cm (mean ± standard deviation) and were found at an average density of 1.57 ± 0.79 to 4.46 ± 3.60 individuals per sq. m. on the bommies. The tetillid sponge population structure remained stable over the course of four years of monitoring. Prokaryotic communities associated with the sponges were distinct but had overlapping functions based on PICRUSt2 predictions. This convergence of functions may reflect enrichment of metabolic processes that are crucial for the survival of the tetillid sponges under prevailing conditions in the reef lagoon. Differentially enriched functions related to carbon, sulfur, fatty acid, and amino acid metabolism, cellular defense, and stress response, may influence the interactions of tetillid sponges with other biota on the bommies.

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Biofilms in premise plumbing systems as a double-edged sword: microbial community composition and functional profiling of biofilms in a tropical region

Journal of Water and Health ◽

10.2166/wh.2020.182 ◽

2020 ◽

Vol 18 (2) ◽

pp. 172-185

Author(s):

Ryan De Sotto ◽

Rena Tang ◽

Sungwoo Bae

Keyword(s):

Microbial Community ◽

Metabolic Pathways ◽

Microbial Community Composition ◽

Microbial Community Analysis ◽

Global Network ◽

Tropical Region ◽

Gene Markers ◽

Premise Plumbing ◽

Functional Profiling ◽

Plumbing Systems

Abstract To understand distributions of opportunistic premise plumbing pathogens (OPPPs) and microbial community structures governed by sample location, pipe materials, water temperature, age of property and type of house, 29 biofilm samples obtained from faucets, pipes, and shower heads in different households in Singapore were examined using next-generation sequencing technology. Predictive functional profiling of the biofilm communities was also performed to understand the potential of uncultivated microorganisms in premise plumbing systems and their involvement in various metabolic pathways. Microbial community analysis showed Proteobacteria, Bacteroidetes, Acidobacteria, Nitrospira, and Actinobacteria to be the most abundant phyla across the samples which was found to be significantly different when grouped by age of the properties, location, and the type of house. Meanwhile, opportunistic premise plumbing pathogens such as Mycobacterium, Citrobacter, Pseudomonas, Stenotrophomonas, and Methylobacterium were observed from the samples at 0.5% of the total reads. Functional prediction using 16S gene markers revealed the involvement of the biofilm communities in different metabolic pathways like nitrogen metabolism, biodegradation of xenobiotics, and bacterial secretion implying diverse functionalities that are yet to be studied in this environment. This study serves as a preliminary survey on the microbial communities harboring premise plumbing systems in a tropical region like Singapore. This article has been made Open Access thanks to the generous support of a global network of libraries as part of the Knowledge Unlatched Select initiative.

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Quantitative and Qualitative β Diversity Measures Lead to Different Insights into Factors That Structure Microbial Communities

Applied and Environmental Microbiology ◽

10.1128/aem.01996-06 ◽

2007 ◽

Vol 73 (5) ◽

pp. 1576-1585 ◽

Cited By ~ 1074

Author(s):

Catherine A. Lozupone ◽

Micah Hamady ◽

Scott T. Kelley ◽

Rob Knight

Keyword(s):

Microbial Community ◽

Microbial Diversity ◽

Community Composition ◽

Microbial Community Composition ◽

Quantitative Measure ◽

Mineral Chemistry ◽

Community Diversity ◽

Data Set ◽

Β Diversity ◽

Unweighted Unifrac

ABSTRACT The assessment of microbial diversity and distribution is a major concern in environmental microbiology. There are two general approaches for measuring community diversity: quantitative measures, which use the abundance of each taxon, and qualitative measures, which use only the presence/absence of data. Quantitative measures are ideally suited to revealing community differences that are due to changes in relative taxon abundance (e.g., when a particular set of taxa flourish because a limiting nutrient source becomes abundant). Qualitative measures are most informative when communities differ primarily by what can live in them (e.g., at high temperatures), in part because abundance information can obscure significant patterns of variation in which taxa are present. We illustrate these principles using two 16S rRNA-based surveys of microbial populations and two phylogenetic measures of community β diversity: unweighted UniFrac, a qualitative measure, and weighted UniFrac, a new quantitative measure, which we have added to the UniFrac website (http://bmf.colorado.edu/unifrac ). These studies considered the relative influences of mineral chemistry, temperature, and geography on microbial community composition in acidic thermal springs in Yellowstone National Park and the influences of obesity and kinship on microbial community composition in the mouse gut. We show that applying qualitative and quantitative measures to the same data set can lead to dramatically different conclusions about the main factors that structure microbial diversity and can provide insight into the nature of community differences. We also demonstrate that both weighted and unweighted UniFrac measurements are robust to the methods used to build the underlying phylogeny.

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Microbial Community Structure and Its Driving Environmental Factors in Black Carp (Mylopharyngodon piceus) Aquaculture Pond

Water ◽

10.3390/w13213089 ◽

2021 ◽

Vol 13 (21) ◽

pp. 3089

Author(s):

Xuemei Li ◽

Lu Liu ◽

Yongjiu Zhu ◽

Tingbing Zhu ◽

Xingbing Wu ◽

...

Keyword(s):

Microbial Community ◽

Pathogenic Bacteria ◽

Pearson Correlation ◽

Microbial Community Composition ◽

Group Method ◽

Strongly Correlated ◽

Microbial Composition ◽

Black Carp ◽

Pair Group ◽

Significant Difference

This study focused on monitoring the dynamics of bacterial communities and assessment of the influences of physicochemical parameters during a culture cycle in black carp polyculture ponds. Our results showed high variation in microbial diversity and microbial composition in the water column during the culture period. Proteobacteria, Actinobacteria, and Bacteroidetes were the most abundant phyla, while the abundances of the phyla Cyanobacteria, Firmicutes, and Bacteroidetes changed in different months. Moreover, 13 abundant genera with significant difference were found between different months. Thus, samples in different months were divided into three groups according to principal coordinate analysis (PCoA) and unweighted pair-group method (UPGMA) clustering results. RDA showed that total nitrogen (TN), total phosphorus (TP), phosphate (PO43−-P), nitrate (NO3−-N), temperature (T), dissolved oxygen (DO), and pH significantly shaped the microbial community composition in different months. While Pearson correlation coefficient showed that T, SD, and pH were strongly correlated to the dominant genera. Considering some genera are potential pathogenic bacteria, we could manage the black carp pond by quickly monitoring the water temperature and SD in the future.

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Switch of fungal to bacterial degradation in natural, drained and rewetted oligotrophic peatlands reflected in <i>δ</i><sup>15</sup>N and fatty acid composition

SOIL ◽

10.5194/soil-6-299-2020 ◽

2020 ◽

Vol 6 (2) ◽

pp. 299-313

Author(s):

Miriam Groß-Schmölders ◽

Pascal von Sengbusch ◽

Jan Paul Krüger ◽

Kristy Klein ◽

Axel Birkholz ◽

...

Keyword(s):

Microbial Community ◽

Stable Isotope ◽

Community Composition ◽

Metabolic Pathways ◽

Turning Point ◽

Microbial Community Composition ◽

Bacterial Degradation ◽

Gram Positive Bacteria ◽

Current State ◽

Cost Efficient

Abstract. For centuries European peatlands have been degrading along with drainage, land use and climate changes. Increasing pressure on peatland ecosystems calls for a more cost-efficient method to indicate the current state of peatlands and the success of restoration efforts. Metabolic pathways in peatland soils are imprinted in stable isotope compositions due to differences in microorganism communities and their metabolic pathways. Therefore, we hypothesize that depth profiles of nitrogen stable isotope values provide a promising opportunity to detect peatland decomposition or restoration. We studied five peatlands, namely Degerö Stormyr (northern Sweden), Lakkasuo (central Finland) and three mires in the Black Forest (southern Germany). At all locations, cores were taken from adjacent drained (or rewetted) and natural sites to identify δ15N trends that could indicate changes due to drainage and restoration. At all drained (and rewetted) sites we found a distinct peak (“turning point”) of the δ15N values in the center of the drained horizon. We did a fatty acids (FAs) analysis to link our results to microbial community composition. As markers, we distinguished between one fungal-derived FA (C18:2ω9c) and four bacterial-derived FAs. For bacteria, we looked for one general bacterial-derived FA (C14:0), two FAs for gram-positive bacteria (i-C15:0; a-C15:0), and one FA for gram-negative bacteria (C16:1ω9c). In accordance with other studies, our results suggest that fungi dominate the microbial metabolism in the upper aerobic peat horizon. This is reflected by depleted δ15N values. Moving downwards, the drained horizon conditions slowly switch to oxygen limitation. Consequently, fungal-derived FAs decrease whereas bacterial-derived FAs rise. The highest diversity of microbial-derived FAs is indicated by the δ15N turning point. Below the δ15N turning point, oxygen is increasingly limited and concentrations of all microbial-derived FAs are decreasing down to the onset of the permanently waterlogged anaerobic horizon. Peatland cores with restoration successes again show, above the formerly drained horizon, no depth trend of the isotopic values. Hence, we conclude that δ15N stable isotope values reflect microbial community composition, which differs between drained and natural peatlands.

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