Diversity of ammonia-oxidising bacteria and archaea in seven different estuarine sediments from Poyang Lake

In the present study, we used a culture-independent method based on library construction and sequencing to analyse the genetic diversity of the ammonia monooxygenase genes (amoA) of ammonia-oxidising archaea and bacteria in seven different estuarine sediments of Poyang Lake. The total of 67 and 38 operational taxonomic units (OTUs) (similarity <95%) of archaeal (AOA) and bacterial (AOB) amoA genes were retrieved respectively. AOA had higher diversity of amoA genes than did AOB. Phylogenetic analysis showed that AOA amoA sequences were closely related to amoA sequences from Crenarchaeota, Thaumarchaeota and some other uncultured archaea. Fragments from AOB were most associated with sequences from betaproteobacteria and some other uncultured bacteria. On the basis of Kendall’s correlation coefficient, there was a significant positive correlation between AOA amoA gene diversity and temperature, and the AOB diversity was positively correlated with total nitrogen and nitrate nitrogen concentration, and negatively correlated with pH in the sediments, suggesting that AOA and AOB were probably sensitive to several environmental factors. Our work could enhance our understanding of the roles of ammonia-oxidising microorganisms in these seven estuarine sediments from Poyang Lake.

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Phylogenetic and Chemical Diversity of a Hybrid-Isoprenoid-Producing Streptomycete Lineage

Applied and Environmental Microbiology ◽

10.1128/aem.01814-13 ◽

2013 ◽

Vol 79 (22) ◽

pp. 6894-6902 ◽

Cited By ~ 13

Author(s):

Kelley A. Gallagher ◽

Kristin Rauscher ◽

Laura Pavan Ioca ◽

Paul R. Jensen

Keyword(s):

Secondary Metabolites ◽

Secondary Metabolite ◽

Sequence Data ◽

Environmental Dna ◽

Chemical Diversity ◽

Phenotypic Trait ◽

Content Type ◽

Operational Taxonomic Units ◽

Culture Independent ◽

Structural Classes

ABSTRACTStreptomycesspecies dedicate a large portion of their genomes to secondary metabolite biosynthesis. A diverse and largely marine-derived lineage within this genus has been designated MAR4 and identified as a prolific source of hybrid isoprenoid (HI) secondary metabolites. These terpenoid-containing compounds are common in nature but rarely observed as bacterial secondary metabolites. To assess the phylogenetic diversity of the MAR4 lineage, complementary culture-based and culture-independent techniques were applied to marine sediment samples collected off the Channel Islands, CA. The results, including those from an analysis of publically available sequence data and strains isolated as part of prior studies, placed 40 new strains in the MAR4 clade, of which 32 originated from marine sources. When combined with sequences cloned from environmental DNA, 28 MAR4 operational taxonomic units (0.01% genetic distance) were identified. Of these, 82% consisted exclusively of either cloned sequences or cultured strains, supporting the complementarity of these two approaches. Chemical analyses of diverse MAR4 strains revealed the production of five different HI structure classes. All 21 MAR4 strains tested produced at least one HI class, with most strains producing from two to four classes. The two major clades within the MAR4 lineage displayed distinct patterns in the structural classes and the number and amount of HIs produced, suggesting a relationship between taxonomy and secondary metabolite production. The production of HI secondary metabolites appears to be a phenotypic trait of the MAR4 lineage, which represents an emerging model with which to study the ecology and evolution of HI biosynthesis.

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Lactococcus lactis Diversity Revealed by Targeted Amplicon Sequencing of purR Gene, Metabolic Comparisons and Antimicrobial Properties in an Undefined Mixed Starter Culture Used for Soft-Cheese Manufacture

Foods ◽

10.3390/foods9050622 ◽

2020 ◽

Vol 9 (5) ◽

pp. 622

Author(s):

Sabrina Saltaji ◽

Olivier Rué ◽

Valérie Sopena ◽

Sophie Sablé ◽

Fatoumata Tambadou ◽

...

Keyword(s):

Microbial Diversity ◽

Starter Culture ◽

Antimicrobial Properties ◽

Amplicon Sequencing ◽

Antimicrobial Activities ◽

Operational Taxonomic Units ◽

Soft Cheese ◽

Culture Independent ◽

Identification Of Species ◽

Species Specific

The undefined mixed starter culture (UMSC) is used in the manufacture of cheeses. Deciphering UMSC microbial diversity is important to optimize industrial processes. The UMSC was studied using culture-dependent and culture-independent based methods. MALDI-TOF MS enabled identification of species primarily from the Lactococcus genus. Comparisons of carbohydrate metabolism profiles allowed to discriminate five phenotypes of Lactococcus (n = 26/1616). The 16S sequences analysis (V1–V3, V3–V4 regions) clustered the UMSC microbial diversity into two Lactococcus operational taxonomic units (OTUs). These clustering results were improved with the DADA2 algorithm on the housekeeping purR sequences. Five L. lactis variants were detected among the UMSC. The whole-genome sequencing of six isolates allowed for the identification of the lactis subspecies using Illumina® (n = 5) and Pacbio® (n = 1) technologies. Kegg analysis confirmed the L. lactis species-specific niche adaptations and highlighted a progressive gene pseudogenization. Then, agar spot tests and agar well diffusion assays were used to assess UMSC antimicrobial activities. Of note, isolate supernatants (n = 34/1616) were shown to inhibit the growth of Salmonella ser. Typhimurium CIP 104115, Lactobacillus sakei CIP 104494, Staphylococcus aureus DSMZ 13661, Enterococcus faecalis CIP103015 and Listeria innocua CIP 80.11. Collectively, these results provide insightful information about UMSC L. lactis diversity and revealed a potential application as a bio-protective starter culture.

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Abundance and composition of ammonia-oxidising bacteria and archaea of a degraded lake wetland, Inner Mongolian Plateau, China

Soil Research ◽

10.1071/sr13160 ◽

2013 ◽

Vol 51 (6) ◽

pp. 554 ◽

Cited By ~ 3

Author(s):

Linhui Wu ◽

Lihua Hui ◽

Xiaoyi Wang ◽

Jingyu Li ◽

Jingli Yu ◽

...

Keyword(s):

Population Size ◽

Community Composition ◽

Chemical Properties ◽

Amoa Gene ◽

Water Withdrawal ◽

Drying Process ◽

Pcr Cloning ◽

Copy Numbers ◽

Drying Up ◽

Ammonia Oxidising Bacteria

Wetlands are one of the most highly threatened ecosystems on Earth, and their loss and degradation are regarded as major environmental problems. The degradation rate of lake wetlands of the Huitengxile grassland, Inner Mongolia, has increased over recent years. In this study, soil samples were collected in a degraded lake wetland of the Huitengxile grassland. The abundance and composition of soil ammonia-oxidising bacteria (AOB) and ammonia-oxidising archaea (AOA) were assessed by quantitative real-time PCR, cloning, and sequencing approaches. Four sampling sites were selected according to the order of water withdrawal. The lakeshore sample appeared to have the highest copy numbers of AOB amoA genes, and the lowest AOB population size was found in the lakebed sample. Similar to AOB, the AOA were most abundant in the lakeshore sample, and the population size in the lake centre sample was the lowest. Ex2cept in one lakebed sample, AOB were more abundant than AOA in all other samples, with AOB to AOA ratios ranging from 11 to 13. Phylogenetic analysis of the amoA gene fragments showed that all AOB sequences from different sites were affiliated to class β-Proteobacteria, order Nitrosomonadales, family Nitrosomonadaceae and can be grouped into two clusters. Little difference was found in AOB community composition among different samples, which indicated that AOB community composition was stable during the drying process of the degraded lake. However, the AOA community compositions were very different between samples. All AOA sequences fell into four clusters. Cluster 1 was dominant in the sample from the centre of the lake, and cluster 2 was dominant in the lakeshore sample, indicating a difference in the community composition of AOA in response to the drying up of the lake. No clear relationship was found between the AOA and AOB community populations and soil physio-chemical properties. This study suggested that the AOA community in wetland systems is more sensitive than the AOB community to the drying process of the wetland ecosystem.

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Seasonal Characterization of the Endophytic Fungal Microbiome of Mulberry (Morus spp.) Cultivars Resistant and Susceptible to Sclerotiniosis

Microorganisms ◽

10.3390/microorganisms9102052 ◽

2021 ◽

Vol 9 (10) ◽

pp. 2052

Author(s):

Weifang Xu ◽

Fei Wang ◽

Ruolin Wang ◽

Yuan Sui ◽

Zeyang Zhou ◽

...

Keyword(s):

Fruit Production ◽

Resistance Level ◽

Operational Taxonomic Units ◽

Mulberry Fruit ◽

Α Diversity ◽

Culture Independent ◽

Morus Spp ◽

Fungal Microbiome ◽

Seasonal Shifts

The endophytic microbiome is thought to play an important role in promoting plant growth and health. Using culture-independent and culture-dependent protocols, this study characterized the seasonal shifts in the endophytic fungal microbiota of four mulberry (Morus L.) cultivars having different levels of resistance to mulberry fruit sclerotiniosis. Core endophytes can be obtained by two approaches, and they were divided into two clusters by season. Spring samples harbored higher operational taxonomic units (OTUs) and α-diversity, while autumn samples had more sequences or isolates of the fungal class Dothideomycetes with the representative orders Capnodiales and Pleosporales. While comparing different mulberry cultivars, we found that the total number of OTUs in susceptible cultivars was higher than that of resistant cultivars, and Cladosporium sp. were observed in all. Notably, the causal agent of fruit sclerotiniosis (Scleromitrula shiraiana) was only detected in susceptible cultivars. Collectively, our work elucidated significant variations in the mulberry endophytic microbiome, mainly because of seasonal shifts, and the fact that the host cultivars and mulberry endophytic fungal community appeared to have a certain connection with the resistance level of mulberry fruit to sclerotiniosis. These results provided valuable information on the isolation and culturing of mulberry endophytes that could be applied to improve mulberry fruit production and health.

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Rare unclassified 16S rRNA operational taxonomic units from the uncharted Engaño Bay (Argentinean Patagonia)

Canadian Journal of Microbiology ◽

10.1139/cjm-2017-0342 ◽

2018 ◽

Vol 64 (1) ◽

pp. 91-96

Author(s):

Andrea Y. Calvo ◽

Julieta M. Manrique ◽

Leandro R. Jones

Keyword(s):

16S Rrna ◽

Community Dynamics ◽

Sequence Data ◽

River Estuary ◽

Fragmented Habitats ◽

Operational Taxonomic Units ◽

Microbial Community Dynamics ◽

Argentinean Patagonia ◽

Culture Independent ◽

Taxonomic Assignments

Rare microbes make up most of the diversity of marine microbiomes, and recent works have highlighted their importance for microbial community dynamics and in fragmented habitats. Rare taxa have been infrequently studied in comparison with abundant groups, and rare unclassified sequences are common in culture-independent studies. Here, we describe a detailed analysis of nonclassifiable sequences from the Chubut river estuary at the Argentinean Patagonia. Standard taxonomic assignments of environmental 16S rRNA sequences resulted in about 13% unclassified operational taxonomic units (OTUs). The potential affiliations of these OTUs could be narrowed by mapping the classification software assignments on a phylogeny obtained directly from our environmental sequence data. Customized BLAST analyses were remarkably consistent with these phylogenetic assignments, especially when the unclassified OTUs were blasted against sequences from cultured and type microorganisms. In addition, our BLAST analyses revealed significant similarities between several unclassified OTUs and a plethora of unclassified sequences from around the world. Further phylogenetic comparisons with 6194 carefully selected reference sequences showed that these unclassified sequences may correspond to 5 unnamed groups, possibly encompassing ranks from subclass to family inside the Alphaproteobacteria, and to an unknown Gracilibacteria lineage. Overall, these results demonstrate the value of straight phylogenetic analysis, customized BLAST searches, and comparisons with sequences from type material, for the systematic study of rare unclassified sequences.

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The Bacterial Microflora of Fish, Revised

The Scientific World JOURNAL ◽

10.1100/tsw.2006.181 ◽

2006 ◽

Vol 6 ◽

pp. 931-945 ◽

Cited By ~ 181

Author(s):

B. Austin

Keyword(s):

Fish Tissue ◽

Taxonomic Composition ◽

Surrounding Water ◽

Complex Molecules ◽

Bacterial Populations ◽

Modern Culture ◽

Light Emitting ◽

Uncultured Bacteria ◽

Culture Independent ◽

Kidney Liver

The results of numerous studies indicate that fish possess bacterial populations on or in their skin, gills, digestive tract, and light-emitting organs. In addition, the internal organs (kidney, liver, and spleen) of healthy fish may contain bacteria, but there is debate about whether or not muscle is actually sterile. Using traditional culture-dependent techniques, the numbers and taxonomic composition of the bacterial populations generally reflect those of the surrounding water. More modern culture-independent approaches have permitted the recognition of previously uncultured bacteria. The role of the organisms includes the ability to degrade complex molecules (therefore exercising a potential benefit in nutrition), to produce vitamins and polymers, and to be responsible for the emission of light by the light-emitting organs of deep-sea fish. Taxa, including Pseudomonas, may contribute to spoilage by the production of histamines in fish tissue.

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Phylogenetic Comparisons of Bacterial Communities from Serpentine and Nonserpentine Soils

Applied and Environmental Microbiology ◽

10.1128/aem.00690-06 ◽

2006 ◽

Vol 72 (11) ◽

pp. 6965-6971 ◽

Cited By ~ 39

Author(s):

David K. Oline

Keyword(s):

16S Rrna ◽

Bacterial Communities ◽

Regional Scale ◽

Serpentine Soils ◽

Operational Taxonomic Units ◽

Microbial Biogeography ◽

Soil Bacterial Communities ◽

Culture Independent ◽

Control Community ◽

16S Rrna Clone Libraries

ABSTRACT I present the results of a culture-independent survey of soil bacterial communities from serpentine soils and adjacent nonserpentine comparator soils using a variety of newly developed phylogenetically based statistical tools. The study design included site-based replication of the serpentine-to-nonserpentine community comparison over a regional scale (∼100 km) in Northern California and Southern Oregon by producing 16S rRNA clone libraries from pairs of samples taken on either side of the serepentine-nonserpentine edaphic boundary at three geographical sites. At the division level, the serpentine and nonserpentine communities were similar to each other and to previous data from forest soils. Comparisons of both richness and Shannon diversity produced no significant differences between any of the libraries, but the vast majority of phylogenetically based tests were significant, even with only 50 sequences per library. These results suggest that most samples were distinct, consisting of a collection of lineages generally not found in other samples. The pattern of results showed that serpentine communities tended to be more similar to each other than they were to nonserpentine communities, and these differences were at a lower taxonomic scale. Comparisons of two nonserpentine communities generally showed differences, and some results suggest that the geographical site may control community composition as well. These results show the power of phylogenetic tests to discern differences between 16S rRNA libraries compared to tests that discard DNA data to bin sequences into operational taxonomic units, and they stress the importance of replication at larger scales for inferences regarding microbial biogeography.

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Assessment of the Microbial Ecology of Ruminal Methanogens in Cattle with Different Feed Efficiencies

Applied and Environmental Microbiology ◽

10.1128/aem.02815-08 ◽

2009 ◽

Vol 75 (20) ◽

pp. 6524-6533 ◽

Cited By ~ 194

Author(s):

Mi Zhou ◽

Emma Hernandez-Sanabria ◽

Le Luo Guan

Keyword(s):

Diversity Indices ◽

Gas Production ◽

Species Variation ◽

Cattle Feed ◽

Methane Gas ◽

Operational Taxonomic Units ◽

Culture Independent ◽

High Feed ◽

Total Dna ◽

The Difference

ABSTRACT Cattle with high feed efficiencies (designated “efficient”) produce less methane gas than those with low feed efficiencies (designated “inefficient”); however, the role of the methane producers in such difference is unknown. This study investigated whether the structures and populations of methanogens in the rumen were associated with differences in cattle feed efficiencies by using culture-independent methods. Two 16S rRNA libraries were constructed using ∼800-bp amplicons generated from pooled total DNA isolated from efficient (n = 29) and inefficient (n = 29) animals. Sequence analysis of up to 490 randomly selected clones from each library showed that the methanogenic composition was variable: less species variation (22 operational taxonomic units [OTUs]) was detected in the rumens of efficient animals, compared to 27 OTUs in inefficient animals. The methanogenic communities in inefficient animals were more diverse than those in efficient ones, as revealed by the diversity indices of 0.84 and 0.42, respectively. Differences at the strain and genotype levels were also observed and found to be associated with feed efficiency in the host. No difference was detected in the total population of methanogens, but the prevalences of Methanosphaera stadtmanae and Methanobrevibacter sp. strain AbM4 were 1.92 (P < 0.05) and 2.26 (P < 0.05) times higher in inefficient animals, while Methanobrevibacter sp. strain AbM4 was reported for the first time to occur in the bovine rumen. Our data indicate that the methanogenic ecology at the species, strain, and/or genotype level in the rumen may play important roles in contributing to the difference in methane gas production between cattle with different feed efficiencies.

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phoDAlkaline Phosphatase Gene Diversity in Soil

Applied and Environmental Microbiology ◽

10.1128/aem.01823-15 ◽

2015 ◽

Vol 81 (20) ◽

pp. 7281-7289 ◽

Cited By ~ 76

Author(s):

Sabine A. Ragot ◽

Michael A. Kertesz ◽

Else K. Bünemann

Keyword(s):

Alkaline Phosphatase ◽

Bacterial Community Structure ◽

Gene Diversity ◽

Organic Phosphorus ◽

454 Sequencing ◽

Environmental Distribution ◽

Content Type ◽

Bacterial Phyla ◽

Operational Taxonomic Units ◽

Different Climates

ABSTRACTPhosphatase enzymes are responsible for much of the recycling of organic phosphorus in soils. The PhoD alkaline phosphatase takes part in this process by hydrolyzing a range of organic phosphoesters. We analyzed the taxonomic and environmental distribution ofphoDgenes using whole-genome and metagenome databases.phoDalkaline phosphatase was found to be spread across 20 bacterial phyla and was ubiquitous in the environment, with the greatest abundance in soil. To study the great diversity ofphoD, we developed a new set of primers which targetsphoDgenes in soil. The primer set was validated by 454 sequencing of six soils collected from two continents with different climates and soil properties and was compared to previously published primers. Up to 685 differentphoDoperational taxonomic units were found in each soil, which was 7 times higher than with previously published primers. The new primers amplified sequences belonging to 13 phyla, including 71 families. The most prevalentphoDgenes identified in these soils were affiliated with the ordersActinomycetales(13 to 35%),Bacillales(1 to 29%),Gloeobacterales(1 to 18%),Rhizobiales(18 to 27%), andPseudomonadales(0 to 22%). The primers also amplifiedphoDgenes from additional orders, includingBurkholderiales,Caulobacterales,Deinococcales,Planctomycetales, andXanthomonadales, which represented the major differences inphoDcomposition between samples, highlighting the singularity of each community. Additionally, thephoDbacterial community structure was strongly related to soil pH, which varied between 4.2 and 6.8. These primers reveal the diversity ofphoDin soil and represent a valuable tool for the study ofphoDalkaline phosphatase in environmental samples.

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New Microbial Biodiversity in Marine Sediments

Annual Review of Marine Science ◽

10.1146/annurev-marine-032020-014552 ◽

2021 ◽

Vol 13 (1) ◽

pp. 161-175 ◽

Cited By ~ 2

Author(s):

Brett J. Baker ◽

Kathryn E. Appler ◽

Xianzhe Gong

Keyword(s):

Microbial Communities ◽

Marine Sediments ◽

Computational Analysis ◽

Gene Diversity ◽

Single Gene ◽

Genomic Data ◽

Global Ocean ◽

Data Sets ◽

Microbial Biodiversity ◽

Uncultured Bacteria

Microbes in marine sediments represent a large portion of the biosphere, and resolving their ecology is crucial for understanding global ocean processes. Single-gene diversity surveys have revealed several uncultured lineages that are widespread in ocean sediments and whose ecological roles are unknown, and advancements in the computational analysis of increasingly large genomic data sets have made it possible to reconstruct individual genomes from complex microbial communities. Using these metagenomic approaches to characterize sediments is transforming our view of microbial communities on the ocean floor and the biodiversity of the planet. In recent years, marine sediments have been a prominent source of new lineages in the tree of life. The incorporation of these lineages into existing phylogenies has revealed that many belong to distinct phyla, including archaeal phyla that are advancing our understanding of the origins of cellular complexity and eukaryotes. Detailed comparisons of the metabolic potentials of these new lineages have made it clear that uncultured bacteria and archaea are capable of mediating key previously undescribed steps in carbon and nutrient cycling.

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