scholarly journals Functional redundancy in natural pico-phytoplankton communities depends on temperature and biogeography

2020 ◽  
Vol 16 (8) ◽  
pp. 20200330
Author(s):  
Duyi Zhong ◽  
Luisa Listmann ◽  
Maria-Elisabetta Santelia ◽  
C-Elisa Schaum
Keyword(s):  
Ecosystem Function ◽  
Functional Redundancy ◽  
Biological Properties ◽  
Community Diversity ◽  
Sampling Location ◽  
Variable Regions ◽  
Carbon Cycles ◽  
Phytoplankton Communities ◽  
Aquatic Food ◽  
Warming World

Biodiversity affects ecosystem function, and how this relationship will change in a warming world is a major and well-examined question in ecology. Yet, it remains understudied for pico-phytoplankton communities, which contribute to carbon cycles and aquatic food webs year-round. Observational studies show a link between phytoplankton community diversity and ecosystem stability, but there is only scarce causal or empirical evidence. Here, we sampled phytoplankton communities from two geographically related regions with distinct thermal and biological properties in the Southern Baltic Sea and carried out a series of dilution/regrowth experiments across three assay temperatures. This allowed us to investigate the effects of loss of rare taxa and establish causal links in natural communities between species richness and several ecologically relevant traits (e.g. size, biomass production, and oxygen production), depending on sampling location and assay temperature. We found that the samples' biogeographical origin determined whether and how functional redundancy changed as a function of temperature for all traits under investigation. Samples obtained from the slightly warmer and more thermally variable regions showed overall high functional redundancy. Samples from the slightly cooler, less variable, stations showed little functional redundancy, i.e. function decreased when species were lost from the community. The differences between regions were more pronounced at elevated assay temperatures. Our results imply that the importance of rare species and the amount of species required to maintain ecosystem function even under short-term warming may differ drastically even within geographically closely related regions of the same ecosystem.

scholarly journals Functional redundancy in natural pico-phytoplankton communities depends on temperature and biogeography

2020 ◽  
Author(s):  
Duyi Zhong ◽  
Luisa Listmann ◽  
Maria-Elisabetta Santelia ◽  
C-Elisa Schaum
Keyword(s):  
Ecosystem Function ◽  
Heat Waves ◽  
Functional Redundancy ◽  
Community Diversity ◽  
Day Length ◽  
Sampling Location ◽  
Major Question ◽  
Variable Regions ◽  
Carbon Cycles ◽  
Phytoplankton Communities

AbstractBiodiversity affects ecosystem function, but how this relationship will pan out in a changing world is still a major question in ecology. It remains especially understudied for pico-phytoplankton communities, which contribute to carbon cycles and aquatic food webs year-round. Observational studies show a link between phytoplankton community diversity and ecosystem stability, but there is only scarce causal or empirical evidence. Here, we sampled phytoplankton communities from two biogeographically distinct (but close enough to not be confounded by differences in day length and precipitation) regions in the Southern Baltic Sea, and carried out a series of dilution/regrowth experiments across three assay temperatures. This allowed us to investigate the effects of loss of rare taxa and establish causal links in natural communities between species richness and several ecologically relevant traits (e.g. size, biomass production, and oxygen production), depending on sampling location and assay temperature. We found that the samples’ bio-geographical origin determined whether and how functional redundancy changed as a function of temperature for all traits under investigation. Samples obtained from the slightly warmer and more thermally variable regions showed overall high functional redundancy. Samples from the slightly cooler, less variable, stations showed little functional redundancy, i.e. function decreased the more species were lost from the community. The differences between regions were more pronounced at elevated assay temperatures. Our results imply that the importance of rare species and the amount of species required to maintain ecosystem function even under short-term warming (e.g. during heat waves) may differ drastically even within geographically closely related regions of the same ecosystem.

scholarly journals Microbial diversity in raw milk and Sayram Ketteki from southern of Xinjiang, China

2021 ◽  
Author(s):  
Dongla Gao ◽  
Weihua Wang ◽  
Zhanjiang Han ◽  
Qian Xi ◽  
Ruicheng Guo ◽  
...  
Keyword(s):  
High Throughput ◽  
Fungal Community ◽  
High Throughput Sequencing ◽  
Principal Component ◽  
Raw Milk ◽  
Fermented Milk ◽  
Community Diversity ◽  
Sampling Location ◽  
Fungal Community Structure ◽  
Microbial Resources

Raw milk and fermented milk are rich in microbial resources, which are essential for the formation of texture, flavor and taste. In order to gain a deeper knowledge of the bacterial and fungal community diversity in local raw milk and home-made yogurts from Sayram town, Baicheng county, Akesu area, southern of Xinjiang, China,30 raw milk and 30 home-made yogurt samples were collected and experiment of high-throughput sequencing was implemented.The results of experiments revealed the species of fungi in raw milk was the most, and the species of bacteria in fermented milk was the least.Based on principal component analysis (PCA), it was found that the bacterial and fungal community structure differed in samples from two types of dairy products.And the presence of 15 bacterial and 12 fungal phyla, comprising 218 bacterial and 495 fungal genera respectively, among all samples. Firmicutes and Ascomycota,Lactobacillus and Candida were the predominant phyla and genera of bacteria and fungi, respectively. The results indicated that the microbial community of raw milk differs from home-made yogurts due to sampling location and manufacturing process. The study suggested that high-throughput sequencing could provide a better understanding of microbiological diversity as well as lay a theoretical foundation for selecting beneficial microbial resources from this natural yogurt.

scholarly journals Evolution of dependoparvoviruses across geological timescales—implications for design of AAV-based gene therapy vectors

2020 ◽  
Vol 6 (2) ◽  
Author(s):  
Evin Hildebrandt ◽  
Judit J Penzes ◽  
Robert J Gifford ◽  
Mavis Agbandje-Mckenna ◽  
Robert M Kotin
Keyword(s):  
Gene Therapy ◽  
In Silico Analysis ◽  
Biological Properties ◽  
Variable Regions ◽  
Evolution Of Viruses ◽  
Extant Species ◽  
Gene Therapy Vectors ◽  
Endogenous Viral Elements ◽  
High Degree ◽  
A2 Domain

Abstract Endogenous viral elements (EVEs) are genetic remnants of viruses that have integrated into host genomes millions of years ago and retained as heritable elements passed on to offspring until present-day. As a result, EVEs provide an opportunity to analyse the genomes of extinct viruses utilizing these genomic viral fossils to study evolution of viruses over large timescales. Analysis of sequences from near full-length EVEs of dependoparvoviral origin identified within three mammalian taxa, Whippomorpha (whales and hippos), Vespertilionidae (smooth-nosed bats), and Lagomorpha (rabbits, hares, and pikas), indicates that distinct ancestral dependoparvovirus species integrated into these host genomes approximately 77 to 23 million years ago. These ancestral viruses are unique relative to modern adeno-associated viruses (AAVs), and distinct from extant species of genus Dependoparvovirus. These EVE sequences show characteristics previously unseen in modern, mammalian AAVs, but instead appear more similar to the more primitive, autonomously replicating and pathogenic waterfowl dependoparvoviruses. Phylogeny reconstruction suggests that the whippomorph EVE orthologue derives from exogenous ancestors of autonomous and highly pathogenic dependoparvovirus lineages, believed to have uniquely co-evolved with waterfowl birds to present date. In contrast, ancestors of the two other mammalian orthologues (Lagomorpha and Vespertilionidae) likely shared the same lineage as all other known mammalian exogenous AAVs. Comparative in silico analysis of the EVE genomes revealed remarkable overall conservation of AAV rep and cap genes, despite millions of years of integration within the host germline. Modelling these proteins identified unexpected variety, even between orthologues, in previously defined capsid viral protein (VP) variable regions, especially in those related to the three- and fivefold symmetry axes of the capsid. Moreover, the normally well-conserved phospholipase A2 domain of the predicted minor VP1 also exhibited a high degree of sequence variance. These findings may indicate unique biological properties for these virus ‘fossils’ relative to extant dependoparvoviruses and suggest key regions to explore within capsid sequences that may confer novel properties for engineered gene therapy vectors based on paleovirology data.

scholarly journals Lake Phytoplankton Assemblage Altered by Irregularly Shaped PLA Body Wash Microplastics but Not by PS Calibration Beads

Water ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 2650
Author(s):  
Kiyoko Yokota ◽  
Marissa Mehlrose
Keyword(s):  
Aquatic Organisms ◽  
Environmental Pollutant ◽  
Taxonomic Composition ◽  
Consumer Products ◽  
Source Water ◽  
Phytoplankton Assemblage ◽  
Phytoplankton Communities ◽  
Aquatic Food ◽  
And Behavior ◽  
Natural Phytoplankton

Microplastics are an emerging environmental pollutant, whose global ubiquity is becoming increasingly evident. Conventional wastewater treatment does not completely remove them, and there are growing concerns about microplastics in source water and post-treatment drinking water. Microplastics have been reported to alter the development, physiology, and behavior of various aquatic organisms; however, limited knowledge exists on their effect on natural phytoplankton communities. Many studies also use uniformly spherical plastic beads, while most scrub particles in consumer products and secondary microplastics in the environment have various shapes and sizes. We tested the effects of two types of microplastics, 50 µm polystyrene (PS) calibration beads and polylactic acid (PLA) plastic body wash scrub particles, and one type of plant-derived body wash scrub particle on a natural phytoplankton assemblage through a 7-day incubation experiment in a temperate, mesotrophic lake. The calibration beads and the plant-derived particles generally did not alter the taxonomic composition of the phytoplankton in the mesocosms, while the PLA body wash microplastics eliminated cryptophytes (p < 0.001) and increased chrysophytes (p = 0.041). Our findings demonstrate differential effects of irregularly shaped PLA body wash microplastics vs. PS calibration beads on lake phytoplankters and empirically support potential bottom-up alteration of the aquatic food web by secondary microplastics.

scholarly journals Accuracy of microbial community diversity estimated by closed- and open-reference OTUs

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3889 ◽  
Author(s):  
Robert C. Edgar
Keyword(s):  
Ribosomal Rna ◽  
De Novo ◽  
Community Diversity ◽  
Reference Database ◽  
Mock Community ◽  
Variable Regions ◽  
Operational Taxonomic Units ◽  
Sequencing Technologies ◽  
Generation Sequencing ◽  
Mock Communities

Next-generation sequencing of 16S ribosomal RNA is widely used to survey microbial communities. Sequences are typically assigned to Operational Taxonomic Units (OTUs). Closed- and open-reference OTU assignment matches reads to a reference database at 97% identity (closed), then clusters unmatched reads using a de novo method (open). Implementations of these methods in the QIIME package were tested on several mock community datasets with 20 strains using different sequencing technologies and primers. Richness (number of reported OTUs) was often greatly exaggerated, with hundreds or thousands of OTUs generated on Illumina datasets. Between-sample diversity was also found to be highly exaggerated in many cases, with weighted Jaccard distances between identical mock samples often close to one, indicating very low similarity. Non-overlapping hyper-variable regions in 70% of species were assigned to different OTUs. On mock communities with Illumina V4 reads, 56% to 88% of predicted genus names were false positives. Biological inferences obtained using these methods are therefore not reliable.

scholarly journals Bacterial Communities in the Rhizosphere and Phyllosphere of Halophytes and Drought-Tolerant Plants in Mediterranean Ecosystems

2020 ◽  
Vol 8 (11) ◽  
pp. 1708
Author(s):  
Savvas Genitsaris ◽  
Natassa Stefanidou ◽  
Kleopatra Leontidou ◽  
Theodora Matsi ◽  
Katerina Karamanoli ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Soil Properties ◽  
Bacterial Communities ◽  
Mediterranean Ecosystems ◽  
Community Diversity ◽  
Sampling Location ◽  
Rrna Gene ◽  
Sodic Soils ◽  
Drought Tolerant ◽  
Tolerant Plants

The aim of the study was to investigate the bacterial community diversity and structure by means of 16S rRNA gene high-throughput amplicon sequencing, in the rhizosphere and phyllosphere of halophytes and drought-tolerant plants in Mediterranean ecosystems with different soil properties. The locations of the sampled plants included alkaline, saline-sodic soils, acidic soils, and the volcanic soils of Santorini Island, differing in soil fertility. Our results showed high bacterial richness overall with Proteobacteria and Actinobacteria dominating in terms of OTUs number and indicated that variable bacterial communities differed depending on the plant’s compartment (rhizosphere and phyllosphere), the soil properties and location of sampling. Furthermore, a shared pool of generalist bacterial taxa was detected independently of sampling location, plant species, or plant compartment. We conclude that the rhizosphere and phyllosphere of native plants in stressed Mediterranean ecosystems consist of common bacterial assemblages contributing to the survival of the plant, while at the same time the discrete soil properties and environmental pressures of each habitat drive the development of a complementary bacterial community with a distinct structure for each plant and location. We suggest that this trade-off between generalist and specialist bacterial community is tailored to benefit the symbiosis with the plant.

scholarly journals Functional Redundancy in Ocean Microbiomes Controls Trait Stability

2021 ◽  
Author(s):  
Taylor M Royalty ◽  
Andrew Decker Steen
Keyword(s):  
Ecosystem Function ◽  
Latent Variable ◽  
Functional Redundancy ◽  
Ecosystem Functions ◽  
Polar Regions ◽  
Microbial Ecosystem ◽  
Physiochemical Parameters ◽  
Β Diversity ◽  
Microbial Ecosystems ◽  
Functional Richness

Advances in nucleic acid sequencing technology have revealed that, in many microbial ecosystems, the same ecosystem function or trait is performed by multiple species or taxa. Theory, developed in the context of macroecology, predicts that communities with high functional redundancy are less likely to lose functions due to species extinction compared to communities with low functional redundancy. It is not clear whether this is the case for microbial communities, particularly on the landscape scale. In part, the lack of quantitative measures for functional redundancy in microbial ecosystems has been prohibitive in addressing this question. We recently proposed a quantitative functional redundancy metric, contribution evenness, which measures how evenly taxa in a community contribute to an ecosystem function or trait. Using transcriptomes deposited in the Ocean Microbial Reference Gene Catalog (OM-RGC.v2), a catalog of genes and transcripts sequenced by the TARA Ocean expedition, we quantified the functional redundancy for 4,314 KEGG Orthologs (KOs) across 124 marine sites. Functional redundancy was highly correlated with a latent variable reflecting few ocean physiochemical parameters and was systematically higher at the poles than in non-polar regions. Functional richness β-diversity among non-polar sites was higher than that among polar sites, indicating that microbial ecosystem functions are more similar among polar sites than among non-polar sites. These observations combined provide evidence that functional redundancy influences microbial ecosystem function stability on spatiotemporal scales consistent with surface ocean mixing. We suggest that future changes in ocean physiochemistry will likely influence this stability.

scholarly journals Increasing N deposition impacts neither diversity nor functions of deadwood-inhabiting fungal communities, but adaptation and functional redundancy ensure ecosystem function

2018 ◽  
Vol 20 (5) ◽  
pp. 1693-1710 ◽  
Author(s):  
Witoon Purahong ◽  
Tesfaye Wubet ◽  
Tiemo Kahl ◽  
Tobias Arnstadt ◽  
Björn Hoppe ◽  
...  
Keyword(s):  
Ecosystem Function ◽  
Functional Redundancy ◽  
N Deposition ◽  
Fungal Communities

scholarly journals A quantitative measure of functional redundancy in microbial ecosystems

2020 ◽  
Author(s):  
Taylor M. Royalty ◽  
Andrew D. Steen
Keyword(s):  
Quantitative Measure ◽  
Functional Redundancy ◽  
Community Diversity ◽  
Phenotypic Traits ◽  
Protein Abundance ◽  
Omics Data ◽  
Ecological Consequence ◽  
Respiration Rates ◽  
Relative Contribution ◽  
Microbial Ecosystems

AbstractAlthough functional redundancy has received increased attention in the microbial ecology literature, no quantitative functional redundancy measurement is currently available which compares multiple communities and integrates of ‘omics data rather than phenotypic traits. Here, we propose an approach for quantifying functional redundancy that use ‘omics data. This approach, termed trait contribution evenness (TCE), is based on traditional measures of community diversity. We measure functional redundancy of a trait within a community as the evenness in relative contribution of that trait among taxa within the community. This definition has several appealing properties including: TCE is an extension of established diversity theory, functional redundancy measurements from communities with different richness and relative trait contribution by taxa are easily comparable, and any quantifiable trait data (genes copies, protein abundance, transcript copies, respiration rates, etc.) is suitable for analysis. Resilience of a trait to taxa extinctions is often viewed as an ecological consequence of traits with high functional redundancy. We demonstrate that TCE functional redundancy is closely and monotonically related to the resilience of a trait to extinctions of trait-bearing taxa. Finally, to illustrate the applicability of TCE, we analyzed the functional redundancy of eight nitrogen-transforming pathways using 2,631 metagenome-assembled genomes from 47 TARA Oceans sites. We found that the NH4+ assimilation pathway was the most functionally redundant (0.6 to 0.7) while nitrification had the lowest functional redundancy (0 to 0.1). Here, TCE functional redundancy addresses shortfalls of other functional redundancy measurements by providing a generalizable, quantitative, and comparable functional redundancy measurement.ImportanceThe broad application of ‘omics technologies in microbiological studies highlights the necessity of integrating traditional ecological theory with omics data when quantifying community functional redundancy. Such an approach should allow for comparisons in functional redundancy between different samples, sites, and studies. Here, we propose measuring functional redundancy based on an expansion of already existing diversity theory. This approach measures how evenly different members in a community contribute to the overall level of a trait within a community. The utility in the approach proposed here will allow for broad evaluation of traits.

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