Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions

Introduction: One of biological wastewater treatment methods that utilizes to both digesting waste activated sludge and methane production is anaerobic digestion (AD). It is believed to be most effective solution in terms of energy crisis and environmental pollution issues. Materials and Methods: In this study the sludge was digested anaerobically sampled from a full-scale WWTP, located at south of Tehran, Iran for evaluation. To study the microbial community within the sludge the MiSeq Sequencing method utilized. Based on our field data (data not shown) and microbial community data, a schematic diagram of probable leading pathways was made in the studied digester. Results: At first, the community variety in the bulk sludge and richness were enhanced followed by loading increasing. Meanwhile, the loading change enhanced the community richness and variety of the sludge. By comparing the rank-abundance distributions, a shallow gradient would show high evenness since the abundances of diverse species are alike. The results showed all the communities were extremely diverse and 15 phyla were distinguished in the sludge sample. The dominant phyla of the community were Bacteroidetes and Firmicutes and quantity of the two phyla were 21% and 11%, respectively. Anaerobaculum, Acinetobacter, Syntrophomonas, and Coprothermobacter were the chief genera for the microbial communities and the sum of four genera were 7%, 3%, 3%, and 2%, respectively. Conclusion: It was shown that syntrophic acetate oxidizing bacterias (SAOBs) metabolized acetate through hydrogen trophic methanogenesis in the digester. Generally, the findings may be useful to help the wastewater operators to utilize an effective method that able to treat waste sludge plus methane production, simultaneously.

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Numerical and taxonomic scale of analysis in paleoecological data sets: Examples from neo-tropical Pleistocene reef coral communities

Journal of Paleontology ◽

10.1017/s0022336000039652 ◽

2001 ◽

Vol 75 (3) ◽

pp. 546-563 ◽

Cited By ~ 9

Author(s):

John M. Pandolfi

Keyword(s):

Reef Coral ◽

Distribution Data ◽

Data Sets ◽

Geographic Scale ◽

Genus Level ◽

Coral Communities ◽

The Caribbean ◽

Presence And Absence ◽

Rank Abundance ◽

Scale Of Analysis

I investigated the degree to which the interpretation of reef coral distribution data is influenced by the numerical and taxonomic scale of analysis in Pleistocene coral communities from the Caribbean Sea. Patterns of community differentiation analyzed at both species and genus levels showed only small differences using different numerical scales (relative abundance, rank abundance and species presence and absence). Whereas some differences were observed between species and genus level patterns, they had little effect on paleoecological interpretations. The greatest differences occurred when presence and absence analyses of assemblages sampled along 40-m transects were compared with those sampled along 40-m transects augmented by a one-hour search for rare taxa. These results suggest that paleoecological interpretations of Quaternary coral communities are robust to numerical scale of analysis at the species and genus level, and to taxonomic scale between the species and genus level. However, interpretations of community structure are sensitive to sampling intensity, geographic scale, and sample size.

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How adaptive immunity constrains the composition and fate of large bacterial populations

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1802887115 ◽

2018 ◽

Vol 115 (32) ◽

pp. E7462-E7468 ◽

Cited By ~ 3

Author(s):

Madeleine Bonsma-Fisher ◽

Dominique Soutière ◽

Sidhartha Goyal

Keyword(s):

Stochastic Dynamics ◽

Phage Genome ◽

Population Level ◽

Abundance Distribution ◽

Stable States ◽

Bacterial Populations ◽

Multiple Stable States ◽

Time Invariant ◽

Microbial Systems ◽

Rank Abundance

Features of the CRISPR-Cas system, in which bacteria integrate small segments of phage genome (spacers) into their DNA to neutralize future attacks, suggest that its effect is not limited to individual bacteria but may control the fate and structure of whole populations. Emphasizing the population-level impact of the CRISPR-Cas system, recent experiments show that some bacteria regulate CRISPR-associated genes via the quorum sensing (QS) pathway. Here we present a model that shows that from the highly stochastic dynamics of individual spacers under QS control emerges a rank-abundance distribution of spacers that is time invariant, a surprising prediction that we test with dynamic spacer-tracking data from literature. This distribution depends on the state of the competing phage–bacteria population, which due to QS-based regulation may coexist in multiple stable states that vary significantly in their phage-to-bacterium ratio, a widely used ecological measure to characterize microbial systems.

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Biotic invasion, niche stability, and the assembly of regional biotas in deep time: comparison between faunal provinces

Paleobiology ◽

10.1017/pab.2016.1 ◽

2016 ◽

Vol 42 (3) ◽

pp. 359-379 ◽

Cited By ~ 3

Author(s):

Mark E. Patzkowsky ◽

Steven M. Holland

Keyword(s):

Late Ordovician ◽

Niche Shift ◽

Time Interval ◽

Natural Experiments ◽

Deep Time ◽

Taconic Orogeny ◽

Ecological Parameters ◽

High Level ◽

Biotic Invasion ◽

Rank Abundance

AbstractBiotic invasions in the fossil record provide natural experiments for testing hypotheses of niche stability, speciation, and the assembly and diversity of regional biotas. We compare ecological parameters (preferred environment, occupancy, median abundance, rank abundance) of genera shared between faunal provinces during the Richmondian Invasion in the Late Ordovician on the Laurentian continent. Genera that spread from one faunal province to the other during the invasion (invading shared genera) have high Spearman rank correlations (>0.5) in three of four ecological parameters, suggesting a high level of niche stability among invaders. Genera that existed in both regions prior to and following the invasion (noninvading shared genera) have low correlations (<0.3) and suggest niche shift between lineages that diverged at least 8 Myr earlier. Niche shift did not accumulate gradually over this time interval but appears to have occurred in a pulse associated with the onset of the Taconic orogeny and the switch from warm-water to cool-water carbonates in southern Laurentia.

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Simultaneously Sparse and Low-Rank Abundance Matrix Estimation for Hyperspectral Image Unmixing

IEEE Transactions on Geoscience and Remote Sensing ◽

10.1109/tgrs.2016.2551327 ◽

2016 ◽

Vol 54 (8) ◽

pp. 4775-4789 ◽

Cited By ~ 36

Author(s):

Paris V. Giampouras ◽

Konstantinos E. Themelis ◽

Athanasios A. Rontogiannis ◽

Konstantinos D. Koutroumbas

Keyword(s):

Hyperspectral Image ◽

Low Rank ◽

Matrix Estimation ◽

Rank Abundance

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The effects of silvicultural disturbances on the diversity of seed-producing plants in the boreal mixedwood forest

Canadian Journal of Forest Research ◽

10.1139/x02-024 ◽

2002 ◽

Vol 32 (7) ◽

pp. 1180-1191 ◽

Cited By ~ 36

Author(s):

F Wayne Bell ◽

Steven G Newmaster

Keyword(s):

Plant Species ◽

Populus Tremuloides ◽

Diversity Indices ◽

Mechanical Equipment ◽

Conifer Species ◽

Mechanical Site Preparation ◽

Clear Cutting ◽

Indigenous Plant ◽

Mechanical Cutting ◽

Rank Abundance

The practice of clear-cutting, followed by site preparing with mechanical equipment, planting a single tree species, and applying herbicides, has recently been cited as a procedure that creates monocultures in northern forests. Research on a trembling aspen (Populus tremuloides Michx.) dominated mixedwood provided an opportunity to examine the potential of silvicultural activities to (i) create monocultures, (ii) create opportunities for the establishment of exotic plant species, and (iii) result in the loss of indigenous plant species. Detailed botanical surveys were conducted for up to 5 years post-treatment in four clearcuts that were mechanically site prepared, planted with a single conifer species, and released with either motor-manual, mechanical, or herbicide treatment. Species richness, abundance (foliar cover), diversity indices, and rank abundance diagrams indicate that the treatments had immediate effects, but none created a monoculture during the period of study. We conclude that the use of clear-cutting, mechanical site preparation, planting a single conifer species, followed by release with motor-manual cutting, mechanical cutting, or herbicide spraying, will not create monocultures in the conditions tested. While 37 exotic species were observed, none of them were tree or shrub species. In addition, no net loss of indigenous seed producing plants was detected. Missed strips and patches, which accounted for up to 25% of the sampled area, buffered treatment effects.

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The control of rank-abundance distributions by a competitive despotic species

Oecologia ◽

10.1007/s00442-014-3060-1 ◽

2014 ◽

Vol 176 (3) ◽

pp. 849-857 ◽

Cited By ~ 6

Author(s):

Ralph Mac Nally ◽

Clive A. McAlpine ◽

Hugh P. Possingham ◽

Martine Maron

Keyword(s):

Rank Abundance

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Spatial Distribution of Rhodopseudomonas palustris Ecotypes on a Local Scale

Applied and Environmental Microbiology ◽

10.1128/aem.69.9.5192-5197.2003 ◽

2003 ◽

Vol 69 (9) ◽

pp. 5192-5197 ◽

Cited By ~ 29

Author(s):

S. J. Bent ◽

C. L. Gucker ◽

Y. Oda ◽

L. J. Forney

Keyword(s):

Spatial Distribution ◽

Rhodopseudomonas Palustris ◽

Sampling Site ◽

Clonal Diversity ◽

Genotypic Diversity ◽

Rrna Gene ◽

Similarity Coefficients ◽

16S Rrna Gene Sequences ◽

Multiple Strains ◽

Rank Abundance

ABSTRACT The number, spatial distribution, and significance of genetically distinguishable ecotypes of prokaryotes in the environment are poorly understood. Oda et al. (Y. Oda, B. Star, L. A. Huisman, J. C. Gottschal, and L. J. Forney, Appl. Environ. Microbiol. 69:xxx-xxx, 2003) have shown that Rhodopseudomonas palustris ecotypes were lognormally distributed along a 10-m transect and that multiple strains of the species could coexist in 0.5-g sediment samples. To extend these observations, we investigated the clonal diversity of R. palustris in 0.5-g samples taken from the corners and center of a 1-m square. A total of 35 or 36 clones were recovered by direct plating from each sample and were characterized by BOX A1R repetitive element-PCR genomic DNA fingerprinting. Isolates with fingerprint images that were ≥80% similar to each other were defined as the same genotype. Among the 178 isolates studied, 32 genotypes were identified, and each genotype contained between 1 and 40 isolates. These clusters were consistent with minor variations found in 16S rRNA gene sequences. The Shannon indices of the genotypic diversity within each location ranged from 1.08 (5 genotypes) to 2.18 (13 genotypes). Comparison of the rank abundance of genotypes found in pairs of locations showed that strains from three locations were similar to each other, with Morisita-Horn similarity coefficients ranging from 0.59 to 0.71. All comparisons involving the remaining two locations resulted in coefficients between 0 and 0.12. From these results we inferred that the patterns of ecotype diversity at the sampling site are patchy at a 1-m scale and postulated that factors such as mixing, competitive interactions, and microhabitat variability are likely to be responsible for the maintenance of the similarities between some locations and the differences between others.

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A comparison of two types of trap for sampling dung beetle populations (Coleoptera: Scarabaeidae)

Bulletin of Entomological Research ◽

10.1017/s0007485300050458 ◽

1990 ◽

Vol 80 (3) ◽

pp. 259-263 ◽

Cited By ~ 13

Author(s):

Bernard M. Doube ◽

Paul S. Giller

Keyword(s):

South Africa ◽

Summer Rainfall ◽

Dung Beetle ◽

Direct Access ◽

Cattle Dung ◽

Pitfall Traps ◽

Significant Difference ◽

Immigration And Emigration ◽

Rank Abundance

AbstractThe effectiveness of pitfall traps baited with cattle dung enclosed in a gauze bag and pads of cattle dung on soil as methods for sampling dung beetle populations was assessed in the summer-rainfall regions of South Africa using 17 species of nocturnal/crepuscular tunnelling beetles. Pitfall traps accumulated the catch and prevented both access to and emigration from the dung bait. In contrast, beetles had direct access to dung pads on soil which allowed colonists to modify the bait and to emigrate. The number of beetles collected was therefore the net result of immigration and emigration. On each of five occasions in November–December 1985, 40 pitfall traps and 40 dung pads were set out in the evening and the trapped beetles recovered the following morning. Overall, 3774 individuals were trapped. For most species there was no significant difference between trap types in the numbers caught but two species were significantly more numerous in pitfall traps and one species was more numerous in the dung pads. However, both methods produced similar patterns of rank abundance of species (r=0.95). There was no evidence that beetles were more evenly distributed between dung pad baits than between pitfall traps.

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