Investigation of the suitability of Remane’s “species minimum” concept in a Mediterranean transitional waters ecosystem

10.7287/peerj.preprints.1549 ◽

2015 ◽

Author(s):

Christina Pavloudi ◽

Anastasis Oulas ◽

Jon B Kristoffersen ◽

Michael W Friedrich ◽

Christos Arvanitidis

Keyword(s):

Salinity Gradient ◽

Environmental Parameters ◽

Taxonomic Diversity ◽

Rrna Gene ◽

Sediment Samples ◽

Open Sea ◽

The Baltic ◽

Water Ecosystems ◽

Shed Light

Remane’s Artenminimum (“species minimum”) concept was developed for the Baltic Sea, the world’s largest semi-enclosed brackish water body with a unique permanent salinity gradient. It argues that taxonomic diversity of macrobenthic organisms is lowest within the horohalinicum, which occurs at salinity 5 to 8, because the number of brackish specialists does not compensate for the decline in marine and freshwater diversity. The aim of the present study was to investigate the sediment bacterial diversity of a transect river-lagoon-open sea, i.e. from freshwater to marine, occurring at Amvrakikos Gulf (Ionian Sea, Western Greece) and to test whether it follows the Remane's concept, both in terms of species composition but also of functionality. DNA was extracted from sediment samples collected in situ from four stations along the aforementioned transect and sequenced for the 16S rRNA gene. In addition, sediment samples were collected for the assessment of benthic macroorganismic diversity. Moreover, several environmental parameters were measured and their correlation with the diversity patterns was explored. The results of the study shed light on the microbial biodiversity of transitional water ecosystems and reveal the effect of salinity on species diversity, both on microorganisms and on macrobenthic organisms.

Download Full-text

Sediment microbial taxonomic and functional diversity in a natural salinity gradient challenge Remane’s “species minimum” concept

PeerJ ◽

10.7717/peerj.3687 ◽

2017 ◽

Vol 5 ◽

pp. e3687 ◽

Cited By ~ 11

Author(s):

Christina Pavloudi ◽

Jon B. Kristoffersen ◽

Anastasis Oulas ◽

Marleen De Troch ◽

Christos Arvanitidis

Keyword(s):

Oxygen Concentration ◽

High Throughput Sequencing ◽

Salinity Gradient ◽

Negative Relationship ◽

Taxonomic Diversity ◽

Rrna Gene ◽

Community Function ◽

Highly Correlated ◽

The Baltic ◽

Taxonomic Groups

Several models have been developed for the description of diversity in estuaries and other brackish habitats, with the most recognized being Remane’s Artenminimum (“species minimum”) concept. It was developed for the Baltic Sea, one of the world’s largest semi-enclosed brackish water body with a unique permanent salinity gradient, and it argues that taxonomic diversity of macrobenthic organisms is lowest within the horohalinicum (5 to 8 psu). The aim of the present study was to investigate the relationship between salinity and sediment microbial diversity at a freshwater-marine transect in Amvrakikos Gulf (Ionian Sea, Western Greece) and assess whether species composition and community function follow a generalized concept such as Remane’s. DNA was extracted from sediment samples from six stations along the aforementioned transect and sequenced for the 16S rRNA gene using high-throughput sequencing. The metabolic functions of the OTUs were predicted and the most abundant metabolic pathways were extracted. Key abiotic variables, i.e., salinity, temperature, chlorophyll-a and oxygen concentration etc., were measured and their relation with diversity and functional patterns was explored. Microbial communities were found to differ in the three habitats examined (river, lagoon and sea) with certain taxonomic groups being more abundant in the freshwater and less in the marine environment, andvice versa. Salinity was the environmental factor with the highest correlation to the microbial community pattern, while oxygen concentration was highly correlated to the metabolic functional pattern. The total number of OTUs showed a negative relationship with increasing salinity, thus the sediment microbial OTUs in this study area do not follow Remane’s concept.

Download Full-text

Environmental parameters of shallow water habitats in the SW Baltic Sea

Earth System Science Data ◽

10.5194/essd-11-947-2019 ◽

2019 ◽

Vol 11 (3) ◽

pp. 947-957 ◽

Cited By ~ 3

Author(s):

Markus Franz ◽

Christian Lieberum ◽

Gesche Bock ◽

Rolf Karez

Keyword(s):

Baltic Sea ◽

Shallow Water ◽

Monitoring Program ◽

Environmental Parameters ◽

Data Availability ◽

Nutrient Concentrations ◽

Baltic Coast ◽

Control Procedures ◽

The Baltic

Abstract. The coastal waters of the Baltic Sea are subject to high variations in environmental conditions, triggered by natural and anthropogenic causes. Thus, in situ measurements of water parameters can be strategic for our understanding of the dynamics in shallow water habitats. In this study we present the results of a monitoring program at low water depths (1–2.5 m), covering 13 stations along the Baltic coast of Schleswig-Holstein, Germany. The provided dataset consists of records for dissolved inorganic nutrient concentrations taken twice a month and continuous readings at 10 min intervals for temperature, salinity and oxygen content. Data underwent quality control procedures and were flagged. On average, a data availability of >90 % was reached for the monitoring period within 2016–2018. The obtained monitoring data reveal great temporal and spatial variabilities of key environmental factors for shallow water habitats in the southwestern Baltic Sea. Therefore the presented information could serve as realistic key data for experimental manipulations of environmental parameters as well as for the development of oceanographic, biogeochemical or ecological models. The data associated with this article can be found at https://doi.org/10.1594/PANGAEA.895257 (Franz et al., 2018).

Download Full-text

Increases in the abundance of microbial genes encoding halotolerance and photosynthesis along a sediment salinity gradient

Biogeosciences ◽

10.5194/bg-9-815-2012 ◽

2012 ◽

Vol 9 (2) ◽

pp. 815-825 ◽

Cited By ~ 18

Author(s):

T. C. Jeffries ◽

J. R. Seymour ◽

K. Newton ◽

R. J. Smith ◽

L. Seuront ◽

...

Keyword(s):

Microbial Community ◽

Dna Sequences ◽

Salinity Gradient ◽

Compatible Solutes ◽

Environmental Parameters ◽

Sediment Samples ◽

Genetic Potential ◽

Genes Encoding ◽

Physical And Chemical ◽

Photosynthesis Gene

Abstract. Biogeochemical cycles are driven by the metabolic activity of microbial communities, yet the environmental parameters that underpin shifts in the functional potential coded within microbial community genomes are still poorly understood. Salinity is one of the primary determinants of microbial community structure and can vary strongly along gradients within a variety of habitats. To test the hypothesis that shifts in salinity will also alter the bulk biogeochemical potential of aquatic microbial assemblages, we generated four metagenomic DNA sequence libraries from sediment samples taken along a continuous, natural salinity gradient in the Coorong lagoon, Australia, and compared them to physical and chemical parameters. A total of 392483 DNA sequences obtained from four sediment samples were generated and used to compare genomic characteristics along the gradient. The most significant shifts along the salinity gradient were in the genetic potential for halotolerance and photosynthesis, which were more highly represented in hypersaline samples. At these sites, halotolerance was achieved by an increase in genes responsible for the acquisition of compatible solutes – organic chemicals which influence the carbon, nitrogen and methane cycles of sediment. Photosynthesis gene increases were coupled to an increase in genes matching Cyanobacteria, which are responsible for mediating CO2 and nitrogen cycles. These salinity driven shifts in gene abundance will influence nutrient cycles along the gradient, controlling the ecology and biogeochemistry of the entire ecosystem.

Download Full-text

Diversity of Pico- to Mesoplankton Along the 2000 km Salinity Gradient of the Baltic Sea

10.1101/035485 ◽

2015 ◽

Cited By ~ 1

Author(s):

Yue OO Hu ◽

Bengt Karlson ◽

Sophie Charvet ◽

Anders F Andersson

Keyword(s):

Baltic Sea ◽

Deep Sequencing ◽

High Throughput Sequencing ◽

Salinity Gradient ◽

Niche Partitioning ◽

Freshwater Ecosystems ◽

Marker Genes ◽

Rrna Gene ◽

The Baltic Sea ◽

The Baltic

Microscopic plankton form the productive base of both marine and freshwater ecosystems and are key drivers of global biogeochemical cycles of carbon and nutrients. Plankton diversity is immense with representations from all major phyla within the three domains of life. So far, plankton monitoring has mainly been based on microscopic identification, which has limited sensitivity and reproducibility, not least because of the numerical majority of plankton being unidentifiable under the light microscope. High-throughput sequencing of taxonomic marker genes offers a means to identify taxa inaccessible by traditional methods; thus, recent studies have unveiled an extensive previously unknown diversity of plankton. Here, we conducted ultra-deep Illumina sequencing (average 105 sequences/sample) of rRNA gene amplicons of surface water eukaryotic and bacterial plankton communities along a 2000 km transect following the salinity gradient of the Baltic Sea. Community composition was strongly correlated with salinity for both bacterial and eukaryotic plankton assemblages, highlighting the importance of salinity for structuring the biodiversity within this ecosystem. The distribution of major planktonic taxa followed expected patterns as observed in monitoring programs, but also novel groups to the Baltic were identified, such as relatives to the coccolithophore Emiliana huxleyi in the northern Baltic Sea. The deep sequencing also enabled accurate enumeration of highly resolved (> 99% identity) operational taxonomic units, which revealed contrasting distribution profiles among closely related populations, reflecting niche partitioning into ecotypes. This study provides the first ultra-deep sequencing-based survey on eukaryotic and bacterial plankton biogeography in the Baltic Sea.

Download Full-text

Diversity and biogeography of Woesearchaeota: A comprehensive analysis of multi-environment data

10.1101/2020.08.09.243345 ◽

2020 ◽

Author(s):

Jing Xiao ◽

Yu Zhang ◽

Wanning Chen ◽

Yanbing Xu ◽

Rui Zhao ◽

...

Keyword(s):

Ribosomal Rna ◽

Core Genome ◽

Environmental Parameters ◽

Taxonomic Diversity ◽

Genomic Diversity ◽

Metabolic Reconstruction ◽

Rrna Gene ◽

Sequencing Data ◽

Rrna Gene Sequencing ◽

Comprehensive Study

AbstractWoesearchaeota is a newly proposed archaeal phylum frequently detected in various environments. Due to the limited systematical study, little is known about their distribution, taxonomy, and metabolism. Here, we conducted a comprehensive study for Woesearchaeota with 16S ribosomal RNA (rRNA) gene sequencing data of 27,709 samples and metagenomic whole genome sequencing (WGS) data of 1,266 samples. We find that apart from free-living environments, Woesearchaeota also widely distribute in host-associated environments. And host-associated environmental parameters greatly affect their distribution. 81 Woesearchaeota genomes, including 33 genomes firstly reconstructed in this project, were assigned to 59 Woesearchaeota species, suggesting their high taxonomic diversity. Comparative analysis indicated that Woesearchaeota have an open pan-genome with small core genome. Metabolic reconstruction showed that particular metabolic pathway absence in specific environments, demonstrated the metabolic diversity of Woesearchaeota varies in differences environments. These results have placed host-associated environments into the global biogeography of Woesearchaeota and have demonstrated their genomic diversity for future investigation of adaptive evolution.

Download Full-text

Increases in the abundance of microbial genes encoding halotolerance and photosynthesis along a sediment salinity gradient

Biogeosciences Discussions ◽

10.5194/bgd-8-7551-2011 ◽

2011 ◽

Vol 8 (4) ◽

pp. 7551-7574 ◽

Cited By ~ 1

Author(s):

T. C. Jeffries ◽

J. R. Seymour ◽

K. Newton ◽

R. J. Smith ◽

L. Seuront ◽

...

Keyword(s):

Microbial Community ◽

Dna Sequences ◽

Salinity Gradient ◽

Compatible Solutes ◽

Environmental Parameters ◽

Sediment Samples ◽

Genetic Potential ◽

Genes Encoding ◽

Physical And Chemical ◽

Photosynthesis Gene

Abstract. Biogeochemical cycles are driven by the metabolic activity of microbial communities, yet the environmental parameters that underpin shifts in the functional potential coded within microbial community genomes are still poorly understood. Salinity is one of the primary determinants of microbial community structure and can vary strongly along gradients within a variety of habitats. To test the hypothesis that shifts in salinity will also alter the bulk biogeochemical potential of aquatic microbial assemblages, we generated four metagenomic DNA sequence libraries from sediment samples taken along a continuous, natural salinity gradient in the Coorong lagoon, Australia, and compared them to physical and chemical parameters. A total of 392483 DNA sequences obtained from four sediment samples were generated and used to compare genomic characteristics along the gradient. The most significant shifts along the salinity gradient were in the genetic potential for halotolerance and photosynthesis, which were more highly represented in hypersaline samples. At these sites, halotolerance was achieved by an increase in genes responsible for the acquisition of compatible solutes – organic chemicals which influence the carbon, nitrogen and methane cycles of sediment. Photosynthesis gene increases were coupled to an increase in genes matching Cyanobacteria, which are responsible for mediating CO2 and nitrogen cycles. These salinity driven shifts in gene abundance will influence nutrient cycles along the gradient, controlling the ecology and biogeochemistry of the entire ecosystem.

Download Full-text

Vibrio Colonization Is Highly Dynamic in Early Microplastic-Associated Biofilms as Well as on Field-Collected Microplastics

Microorganisms ◽

10.3390/microorganisms9010076 ◽

2020 ◽

Vol 9 (1) ◽

pp. 76

Author(s):

Katharina Kesy ◽

Matthias Labrenz ◽

Brittan S. Scales ◽

Bernd Kreikemeyer ◽

Sonja Oberbeckmann

Keyword(s):

Aquatic Ecosystems ◽

Operational Taxonomic Unit ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Incubation Experiment ◽

The Baltic Sea ◽

In Situ Incubation ◽

The Baltic

Microplastics are ubiquitous in aquatic ecosystems and provide a habitat for biofilm-forming bacteria. The genus Vibrio, which includes potential pathogens, was detected irregularly on microplastics. Since then, the potential of microplastics to enrich (and serve as a vector for) Vibrio has been widely discussed. We investigated Vibrio abundance and operational taxonomic unit (OTU) composition on polyethylene and polystyrene within the first 10 h of colonization during an in situ incubation experiment, along with those found on particles collected from the Baltic Sea. We used 16S rRNA gene amplicon sequencing and co-occurrence networks to elaborate the role of Vibrio within biofilms. Colonization of plastics with Vibrio was detectable after one hour of incubation; however, Vibrio numbers and composition were very dynamic, with a more stable population at the site with highest nutrients and lowest salinity. Likewise, Vibrio abundances on field-collected particles were variable but correlated with proximity to major cities. Vibrio was poorly connected within biofilm networks. Taken together, this indicates that Vibrio is an early colonizer of plastics, but that the process is undirected and independent of the specific surface. Still, higher nutrients could enhance a faster establishment of Vibrio populations. These parameters should be considered when planning studies investigating Vibrio on microplastics.

Download Full-text

Distribution of PAHs and the PAH-degrading bacteria in the deep-sea sediments of the high-latitude Arctic Ocean

Biogeosciences ◽

10.5194/bg-12-2163-2015 ◽

2015 ◽

Vol 12 (7) ◽

pp. 2163-2177 ◽

Cited By ~ 42

Author(s):

C. Dong ◽

X. Bai ◽

H. Sheng ◽

L. Jiao ◽

H. Zhou ◽

...

Keyword(s):

Arctic Ocean ◽

Deep Sea ◽

The Arctic ◽

Rrna Gene ◽

Sediment Samples ◽

Pah Degradation ◽

Degrading Bacteria ◽

The Arctic Ocean ◽

Deep Sea Sediments

Abstract. Polycyclic aromatic hydrocarbons (PAHs) are common organic pollutants that can be transferred long distances and tend to accumulate in marine sediments. However, less is known regarding the distribution of PAHs and their natural bioattenuation in the open sea, especially the Arctic Ocean. In this report, sediment samples were collected at four sites from the Chukchi Plateau to the Makarov Basin in the summer of 2010. PAH compositions and total concentrations were examined with GC-MS. The concentrations of 16 EPA-priority PAHs varied from 2.0 to 41.6 ng g−1 dry weight and decreased with sediment depth and movement from the southern to the northern sites. Among the targeted PAHs, phenanthrene was relatively abundant in all sediments. The 16S rRNA gene of the total environmental DNA was analyzed with Illumina high-throughput sequencing (IHTS) to determine the diversity of bacteria involved in PAH degradation in situ. The potential degraders including Cycloclasticus, Pseudomonas, Halomonas, Pseudoalteromonas, Marinomonas, Bacillus, Dietzia, Colwellia, Acinetobacter, Alcanivorax, Salinisphaera and Shewanella, with Dietzia as the most abundant, occurred in all sediment samples. Meanwhile, enrichment with PAHs was initiated onboard and transferred to the laboratory for further enrichment and to obtain the degrading consortia. Most of the abovementioned bacteria in addition to Hahella, Oleispira, Oceanobacter and Hyphomonas occurred alternately as predominant members in the enrichment cultures from different sediments based on IHTS and PCR-DGGE analysis. To reconfirm their role in PAH degradation, 40 different bacteria were isolated and characterized, among which Cycloclasticus Pseudomonas showed the best degradation capability under low temperatures. Taken together, PAHs and PAH-degrading bacteria were widespread in the deep-sea sediments of the Arctic Ocean. We propose that bacteria of Cycloclasticus, Pseudomonas, Pseudoalteromonas, Halomonas, Marinomonas and Dietzia may play the most important role in PAH mineralization in situ.

Download Full-text

A Differential Metabarcoding Approach to Describe Taxonomy Profiles of Bacteria and Archaea in the Saltern of Margherita di Savoia (Italy)

Microorganisms ◽

10.3390/microorganisms8060936 ◽

2020 ◽

Vol 8 (6) ◽

pp. 936 ◽

Cited By ~ 2

Author(s):

Claudia Leoni ◽

Mariateresa Volpicella ◽

Bruno Fosso ◽

Caterina Manzari ◽

Elisabetta Piancone ◽

...

Keyword(s):

Ecological Model ◽

Salinity Range ◽

Rrna Gene ◽

Hypervariable Regions ◽

Cell Counts ◽

Precious Resource ◽

Catalyzed Reporter Deposition ◽

Card Fish ◽

The 16S Rrna Gene

Microorganisms inhabiting saline environments are an interesting ecological model for the study of the adaptation of organisms to extreme living conditions and constitute a precious resource of enzymes and bioproducts for biotechnological applications. We analyzed the microbial communities in nine ponds with increasing salt concentrations (salinity range 4.9–36.0%) of the Saltern of Margherita di Savoia (Italy), the largest thalassohaline saltern in Europe. A deep-metabarcoding NGS procedure addressing separately the V5-V6 and V3-V4 hypervariable regions of the 16S rRNA gene of Bacteria and Archaea, respectively, and a CARD-FISH (catalyzed reporter deposition fluorescence in situ hybridization) analysis allowed us to profile the dynamics of microbial populations at the different salt concentrations. Both the domains were detected throughout the saltern, even if the low relative abundance of Archaea in the three ponds with the lowest salinities prevented the construction of the relative amplicon libraries. The highest cell counts were recorded at 14.5% salinity for Bacteria and at 24.1% salinity for Archaea. While Bacteria showed the greatest number of genera in the first ponds (salinity range 4.9–14.5%), archaeal genera were more numerous in the last ponds of the saltern (salinity 24.1–36.0%). Among prokaryotes, Salinibacter was the genus with the maximum abundance (~49% at 34.6% salinity). Other genera detected at high abundance were the archaeal Haloquadratum (~43% at 36.0% salinity) and Natronomonas (~18% at 13.1% salinity) and the bacterial “Candidatus Aquiluna” (~19% at 14.5% salinity). Interestingly, “Candidatus Aquiluna” had not been identified before in thalassohaline waters.

Download Full-text