scholarly journals Microbial loop of a Proterozoic ocean analogue

2021 ◽  
Author(s):  
Jaspreet S Saini ◽  
Christel Hassler ◽  
Rachel Cable ◽  
Marion Fourquez ◽  
Francesco Danza ◽  
...  
Keyword(s):  
Organic Matter ◽  
Secondary Production ◽  
Microbial Loop ◽  
Biological Data ◽  
Rrna Gene ◽  
Data Types ◽  
Sulfur Bacteria ◽  
Eukaryotic Phytoplankton ◽  
Essential Components ◽  
Parachlorella Kessleri

AbstractMeromictic Lake Cadagno, an ancient ocean analogue, is known for its permanent stratification and persistent anoxygenic microbial bloom within the chemocline. Although the anaerobic microbial ecology of the lake has been extensively studied for at least 25 years, a comprehensive picture of the microbial food web linking the bacterial layer to phytoplankton and viruses, with explicit measures of primary and secondary production, is still missing. This study sought to understand better the abundances and productivity of microbes in the context of nutrient biogeochemical cycling across the stratified zones of Lake Cadagno. Photosynthetic pigments and chloroplast 16S rRNA gene phylogenies suggested the presence of eukaryotic phytoplankton through the water column. Evidence supported high abundances of Ankyra judayi, a high-alpine adapted chlorophyte, in the oxic mixolimnion where oxygenic-primary production peaked. Through the low- and no-oxygen chemocline and monimolimnion, chlorophytes related to Closteriopsis acicularis, a known genus of meromictic lakes, and Parachlorella kessleri were observed. Chromatium, anoxygenic phototrophic sulfur bacteria, dominated the chemocline along with Lentimicrobium, a genus of known fermenters whose abundance was newly reported in Lake Cadagno. Secondary production peaked in the chemocline suggesting primary producers depend on heterotrophs for nutrient remineralization. As previously observed, sulfur-reducing bacteria (SRBs), especially Desulfocapsa and Desulfobulbus, were present in the chemocline and anoxic monimolimnion. Virus-to-microbe ratios (VMR) peaked in the zone of phytoplankton yet were at a minimum at the peak of Chromatium. These dynamic trends suggest viruses may play a role in the modulation of oxygenic and anoxygenic photo- and chemosynthesis in Lake Cadagno and other permanently stratified systems.ImportanceAs a window to the past, the study offers insights into the role of microbial guilds of Proterozoic ocean chemoclines in the production and recycling of organic matter of sulfur- and ammonia-containing ancient oceans. The new observations described here suggest that eukaryotic algae were persistent in the low oxygen upper-chemocline in association with purple and green sulfur bacteria in the lower half of the chemocline. Further, this study provides the first insights into Lake Cadagno viral ecology. High viral abundances suggested viruses may be essential components of the chemocline where their activity may result in the release and recycling of organic matter. The framework developed in this study through the integration of diverse geochemical and biological data types lays the foundation for future studies to quantitatively resolve the processes performed by discrete populations comprising the microbial loop in this early anoxic ocean analogue.

scholarly journals Bacterial, phytoplankton, and viral dynamics of meromictic Lake Cadagno offer insights into the Proterozoic ocean microbial loop

2021 ◽  
Author(s):  
Jaspreet Singh Saini ◽  
Christel Hassler ◽  
Rachel N Cable ◽  
Marion Fourquez ◽  
Francesco Danza ◽  
...  
Keyword(s):  
Meromictic Lake ◽  
Close Relative ◽  
Rrna Gene ◽  
Viral Dynamics ◽  
Comprehensive Understanding ◽  
Sulfur Bacteria ◽  
Eukaryotic Phytoplankton ◽  
Simultaneous Study ◽  
New Perspective ◽  
Secondary Productivity

Meromictic Lake Cadagno, with its permanent stratification and persistent microbial bloom within the anoxic chemocline, serves as an ancient ocean analogue. Although the lake has been studied for over 25 years, the absence of simultaneous study of the bacteria, phytoplankton, and viruses, together with primary and secondary productivity, has hindered a comprehensive understanding of its microbial food web. This study evaluated the identities, abundances, and productivity of microbes in the context of nutrient biogeochemical cycling across the stratified depths of Lake Cadagno. Photosynthetic pigments and chloroplast 16S rRNA gene phylogenies suggested high abundances of eukaryotic phytoplankton, primarily Chlorophyta, through the water column. Of these, a close relative of Ankyra judayi, a high-alpine adapted chlorophyte, peaked with oxygen in the mixolimnion, while Closteriopsis-related chlorophytes peaked in the chemocline and monimolimnion. Chromatium, a genus of anoxygenic phototrophic sulfur bacteria, dominated the chemocline along with Lentimicrobium, a genus of known fermenters whose abundance was newly reported in Lake Cadagno. Secondary production peaked in the chemocline, suggesting anoxygenic primary producers depended on heterotrophic nutrient remineralization. Virus-to-microbe ratios (VMR) peaked in the zone of high phytoplankton abundances, yet were at a minimum at the peak of Chromatium, dynamic trends that suggest viruses may play a role in the modulation of oxygenic and anoxygenic photo- and chemosynthesis in Lake Cadagno. Through the combined analysis of bacterial, eukaryotic, viral, and biogeochemical dynamics of Lake Cadagno, this study provides a new perspective on the biological and geochemical connections that comprised the food webs of the Proterozoic ocean.

Physico-Chemical Properties of Soil Collected from Chandrabhaga River in Kalmeshwar, Nagpur, Maharashtra

2020 ◽  
Vol 07 (02) ◽  
pp. 1-3
Author(s):  
Amita M Watkar ◽  
Keyword(s):  
Organic Matter ◽  
Soil Quality ◽  
Agricultural Land ◽  
Organic Matter Content ◽  
Chemical Properties ◽  
Matter Content ◽  
Soil Attributes ◽  
Essential Components ◽  
Agricultural Land Management ◽  
Physical And Chemical

Soil, itself means Soul of Infinite Life. Soil is the naturally occurring unconsolidated or loose covering on the earth’s surface. Physical properties depend upon the amount, size, shape, arrangement, and mineral composition of soil particles. It also depends on the organic matter content and pore spaces. Chemical properties depend on the Inorganic and organic matter present in the soil. Soils are the essential components of the environment and foundation resources for nearly all types of land use, besides being the most important component of sustainable agriculture. Therefore, assessment of soil quality and its direction of change with time is an ideal and primary indicator of sustainable agricultural land management. Soil quality indicators refer to measurable soil attributes that influence the capacity of a soil to function, within the limits imposed by the ecosystem, to preserve biological productivity and environmental quality and promote plant, animal and human health. The present study is to assess these soil attributes such as physical and chemical properties season-wise.

scholarly journals 18S rRNA gene sequences of leptocephalus gut contents, particulate organic matter, and biological oceanographic conditions in the western North Pacific

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tsuyoshi Watanabe ◽  
Satoshi Nagai ◽  
Yoko Kawakami ◽  
Taiga Asakura ◽  
Jun Kikuchi ◽  
...  
Keyword(s):  
Organic Matter ◽  
Particulate Organic Matter ◽  
North Pacific ◽  
Western North Pacific ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
Gut Contents ◽  
Rrna Gene ◽  
Marine Snow ◽  
Chlorophyll Maximum

AbstractEel larvae apparently feed on marine snow, but many aspects of their feeding ecology remain unknown. The eukaryotic 18S rRNA gene sequence compositions in the gut contents of four taxa of anguilliform eel larvae were compared with the sequence compositions of vertically sampled seawater particulate organic matter (POM) in the oligotrophic western North Pacific Ocean. Both gut contents and POM were mainly composed of dinoflagellates as well as other phytoplankton (cryptophytes and diatoms) and zooplankton (ciliophoran and copepod) sequences. Gut contents also contained cryptophyte and ciliophoran genera and a few other taxa. Dinoflagellates (family Gymnodiniaceae) may be an important food source and these phytoplankton were predominant in gut contents and POM as evidenced by DNA analysis and phytoplankton cell counting. The compositions of the gut contents were not specific to the species of eel larvae or the different sampling areas, and they were most similar to POM at the chlorophyll maximum in the upper part of the thermocline (mean depth: 112 m). Our results are consistent with eel larvae feeding on marine snow at a low trophic level, and feeding may frequently occur in the chlorophyll maximum in the western North Pacific.

scholarly journals Respiration of 13C-Labeled Substrates Added to Soil in the Field and Subsequent 16S rRNA Gene Analysis of 13C-Labeled Soil DNA

2003 ◽  
Vol 69 (3) ◽  
pp. 1614-1622 ◽  
Author(s):  
P. Padmanabhan ◽  
S. Padmanabhan ◽  
C. DeRito ◽  
A. Gray ◽  
D. Gannon ◽  
...  
Keyword(s):  
Organic Matter ◽  
Soil Organic Matter ◽  
16S Rrna ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Gas Chromatography Mass Spectrometry ◽  
Rrna Gene ◽  
Labeled Compounds ◽  
Field Soil ◽  
Soil Dna

ABSTRACT Our goal was to develop a field soil biodegradation assay using 13C-labeled compounds and identify the active microorganisms by analyzing 16S rRNA genes in soil-derived 13C-labeled DNA. Our biodegradation approach sought to minimize microbiological artifacts caused by physical and/or nutritional disturbance of soil associated with sampling and laboratory incubation. The new field-based assay involved the release of 13C-labeled compounds (glucose, phenol, caffeine, and naphthalene) to soil plots, installation of open-bottom glass chambers that covered the soil, and analysis of samples of headspace gases for 13CO2 respiration by gas chromatography/mass spectrometry (GC/MS). We verified that the GC/MS procedure was capable of assessing respiration of the four substrates added (50 ppm) to 5 g of soil in sealed laboratory incubations. Next, we determined background levels of 13CO2 emitted from naturally occurring soil organic matter to chambers inserted into our field soil test plots. We found that the conservative tracer, SF6, that was injected into the headspace rapidly diffused out of the soil chamber and thus would be of little value for computing the efficiency of retaining respired 13CO2. Field respiration assays using all four compounds were completed. Background respiration from soil organic matter interfered with the documentation of in situ respiration of the slowly metabolized (caffeine) and sparingly soluble (naphthalene) compounds. Nonetheless, transient peaks of 13CO2 released in excess of background were found in glucose- and phenol-treated soil within 8 h. Cesium-chloride separation of 13C-labeled soil DNA was followed by PCR amplification and sequencing of 16S rRNA genes from microbial populations involved with 13C-substrate metabolism. A total of 29 full sequences revealed that active populations included relatives of Arthrobacter, Pseudomonas, Acinetobacter, Massilia, Flavobacterium, and Pedobacter spp. for glucose; Pseudomonas, Pantoea, Acinetobacter, Enterobacter, Stenotrophomonas, and Alcaligenes spp. for phenol; Pseudomonas, Acinetobacter, and Variovorax spp. for naphthalene; and Acinetobacter, Enterobacter, Stenotrophomonas, and Pantoea spp. for caffeine.

scholarly journals Functional and Structural Responses of Hyporheic Biofilms to Varying Sources of Dissolved Organic Matter

2014 ◽  
Vol 80 (19) ◽  
pp. 6004-6012 ◽  
Author(s):  
Karoline Wagner ◽  
Mia M. Bengtsson ◽  
Katharina Besemer ◽  
Anna Sieczko ◽  
Nancy R. Burns ◽  
...  
Keyword(s):  
Organic Matter ◽  
16S Rrna ◽  
Dissolved Organic Matter ◽  
Community Composition ◽  
Hyporheic Zone ◽  
Priority Effects ◽  
Stream Ecosystems ◽  
Rrna Gene ◽  
Structural Responses

ABSTRACTHeadwater streams are tightly connected with the terrestrial milieu from which they receive deliveries of organic matter, often through the hyporheic zone, the transition between groundwater and streamwater. Dissolved organic matter (DOM) from terrestrial sources (that is, allochthonous) enters the hyporheic zone, where it may mix with DOM fromin situproduction (that is, autochthonous) and where most of the microbial activity takes place. Allochthonous DOM is typically considered resistant to microbial metabolism compared to autochthonous DOM. The composition and functioning of microbial biofilm communities in the hyporheic zone may therefore be controlled by the relative availability of allochthonous and autochthonous DOM, which can have implications for organic matter processing in stream ecosystems. Experimenting with hyporheic biofilms exposed to model allochthonous and autochthonous DOM and using 454 pyrosequencing of the 16S rRNA (targeting the “active” community composition) and of the 16S rRNA gene (targeting the “bulk” community composition), we found that allochthonous DOM may drive shifts in community composition whereas autochthonous DOM seems to affect community composition only transiently. Our results suggest that priority effects based on resource-driven stochasticity shape the community composition in the hyporheic zone. Furthermore, measurements of extracellular enzymatic activities suggest that the additions of allochthonous and autochthonous DOM had no clear effect on the function of the hyporheic biofilms, indicative of functional redundancy. Our findings unravel possible microbial mechanisms that underlie the buffering capacity of the hyporheic zone and that may confer stability to stream ecosystems.

A Latent Feature Model Approach to Biclustering

2016 ◽  
Vol 6 (2) ◽  
pp. 11-28
Author(s):  
José Caldas ◽  
Samuel Kaski
Keyword(s):  
Expectation Maximization Algorithm ◽  
Learning Task ◽  
Biological Data ◽  
Feature Model ◽  
Data Matrix ◽  
Data Types ◽  
Data Set ◽  
Modelling Framework ◽  
Number Variation ◽  
Mirna Expression Data

Biclustering is the unsupervised learning task of mining a data matrix for useful submatrices, for instance groups of genes that are co-expressed under particular biological conditions. As these submatrices are expected to partly overlap, a significant challenge in biclustering is to develop methods that are able to detect overlapping biclusters. The authors propose a probabilistic mixture modelling framework for biclustering biological data that lends itself to various data types and allows biclusters to overlap. Their framework is akin to the latent feature and mixture-of-experts model families, with inference and parameter estimation being performed via a variational expectation-maximization algorithm. The model compares favorably with competing approaches, both in a binary DNA copy number variation data set and in a miRNA expression data set, indicating that it may potentially be used as a general-problem solving tool in biclustering.

Bio-Inspired Algorithms in Bioinformatics I

2011 ◽  
pp. 236-240
Author(s):  
José Antonio Seoane Fernández ◽  
Mónica Miguélez Rico
Keyword(s):  
Human Genome ◽  
Heterogeneous Data ◽  
Genome Project ◽  
Biological Data ◽  
Organizational Level ◽  
Data Types ◽  
Proteomic Data ◽  
New Information ◽  
Cell Tissue ◽  
The Human Genome Project

Large worldwide projects like the Human Genome Project, which in 2003 successfully concluded the sequencing of the human genome, and the recently terminated Hapmap Project, have opened new perspectives in the study of complex multigene illnesses: they have provided us with new information to tackle the complex mechanisms and relationships between genes and environmental factors that generate complex illnesses (Lopez, 2004; Dominguez, 2006). Thanks to these new genomic and proteomic data, it becomes increasingly possible to develop new medicines and therapies, establish early diagnoses, and even discover new solutions for old problems. These tasks however inevitably require the analysis, filtration, and comparison of a large amount of data generated in a laboratory with an enormous amount of data stored in public databases, such as the NCBI and the EBI. Computer sciences equip biomedicine with an environment that simplifies our understanding of the biological processes that take place in each and every organizational level of live matter (molecular level, genetic level, cell, tissue, organ, individual, and population) and the intrinsic relationships between them. Bioinformatics can be described as the application of computational methods to biological discoveries (Baldi, 1998). It is a multidisciplinary area that includes computer sciences, biology, chemistry, mathematics, and statistics. The three main tasks of bioinformatics are the following: develop algorithms and mathematical models to test the relationships between the members of large biological datasets, analyze and interpret heterogeneous data types, and implement tools that allow the storage, retrieve, and management of large amounts of biological data.

Impact of sea level change on coastal soil organic matter, priming effects and prokaryotic community assembly

2019 ◽  
Vol 95 (10) ◽  
Author(s):  
Thomas Dinter ◽  
Simone Geihser ◽  
Matthias Gube ◽  
Rolf Daniel ◽  
Yakov Kuzyakov
Keyword(s):  
Organic Matter ◽  
Salt Marsh ◽  
Soil Organic Matter ◽  
Salt Marshes ◽  
Extracellular Enzymes ◽  
Rrna Gene ◽  
Co2 Efflux ◽  
Prokaryotic Community ◽  
Priming Effects ◽  
Niche Adaptation

ABSTRACT Salt marshes are coastal areas storing high amounts of soil organic matter (SOM) while simultaneously being prone to tidal changes. Here, SOM-decomposition and accompanied priming effects (PE), which describe interactions between labile and old SOM, were studied under controlled flooding conditions. Soil samples from two Wadden Sea salt marsh zones, pioneer (Pio), flooded two times/day, and lower salt marsh (Low), flooded ∼eight times/month, were measured for 56 days concerning CO2-efflux and prokaryotic community shifts during three different inundation-treatments: total-drained (Drained), all-time-flooded (Waterlogged) or temporal-flooding (Tidal). Priming was induced by 14C-glucose addition. CO2-efflux from soil followed Low>Pio and Tidal>Drained>Waterlogged, likely due to O2-depletion and moisture maintenance, two key factors governed by tidal inundation with regard to SOM mineralisation. PEs in both zones were positive (Drained) or absent (Waterlogged, Tidal), presumably as a result of prokaryotes switching from production of extracellular enzymes to direct incorporation of labile C. A doubled amount of prokaryotic biomass in Low compared to Pio probably induced higher chances of cometabolic effects and higher PE. 16S-rRNA-gene-amplicon-based analysis revealed differences in bacterial and archaeal community composition between both zones, revealing temporal niche adaptation with flooding treatment. Strongest alterations were found in Drained, likely due to inundation-mediated changes in C-binding capacities.

scholarly journals Changes in the structure and function of the North Sea fish foodweb, 1973–2000, and the impacts of fishing and climate

2005 ◽  
Vol 62 (5) ◽  
pp. 847-868 ◽  
Author(s):  
Michael R. Heath
Keyword(s):  
North Sea ◽  
Secondary Production ◽  
Demersal Fish ◽  
Biological Data ◽  
Similar Species ◽  
The North ◽  
Production And Consumption ◽  
The North Sea ◽  
Vacant Niches ◽  
And Function

Abstract North Sea environmental and biological data were analysed to examine 30-year changes in production and consumption in the fish foodweb. The analysis revealed that the demand for secondary production placed on the ecosystem by fish declined from approximately 20 g C m−2 y−1 in the 1970s to 16 g C m−2 y−1 in the 1990s. Over the same period, the proportion of demand provided by zooplankton production increased from around 70% to 75%. The overall decrease was mainly due to a reduction in piscivorous demersal fish. Average secondary production by omnivorous zooplankton was estimated to be 35 g C m−2 y−1, and annual fluctuations were positively correlated with the gross production of planktivorous fish. The results suggest a “bottom-up” control of the pelagic foodweb. Individual planktivore species have been impacted by fishing, but the populations of other functionally similar species have expanded to fill the vacant niches, thus maintaining the planktivore role in the system. In contrast, the results indicate that benthos production was more “top-down” controlled. Overall, demersal fish species have been depleted by fishing, with no obvious species expansions to fill the vacant niche, releasing the benthos from predation pressure, and leading to an increase in benthic production and fisheries for invertebrates.

scholarly journals Thiocystis chemoclinalis sp. nov. and Thiocystis cadagnonensis sp. nov., motile purple sulfur bacteria isolated from the chemocline of a meromictic lake

2011 ◽  
Vol 61 (7) ◽  
pp. 1682-1687 ◽  
Author(s):  
Sandro Peduzzi ◽  
Allana Welsh ◽  
Antonella Demarta ◽  
Paola Decristophoris ◽  
Raffaele Peduzzi ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Phylogenetic Analyses ◽  
Distinct Species ◽  
Meromictic Lake ◽  
Purple Sulfur Bacteria ◽  
Rrna Gene ◽  
Bacterial Populations ◽  
Sulfur Bacteria ◽  
Type Strains ◽  
Sequence Similarities

Two isolates, designated CadH11T and Cad448T, representing uncultured purple sulfur bacterial populations H and 448, respectively, in the chemocline of Lake Cadagno, a crenogenic meromictic lake in Switzerland, were obtained using enrichment and isolation conditions that resembled those used for cultured members of the genus Thiocystis. Phenotypic, genotypic and phylogenetic analyses of these isolates confirmed their assignment to the genus Thiocystis. However, 16S rRNA gene sequence similarities of 98.2 % between CadH11T and Cad448T, and similarities of 97.7 and 98.5 %, respectively, with their closest cultured relative Thiocystis gelatinosa DSM 215T, as well as differences in DNA G+C content and carbon source utilization suggested that the isolates belonged to two distinct species. DNA–DNA hybridization of CadH11T and Cad448T with T. gelatinosa DSM 215T showed relatedness values of 46.4 and 60.8 %, respectively; the relatedness value between CadH11T and Cad448T was 59.2 %. Based on this evidence, strains CadH11T and Cad448T represent two novel species within the genus Thiocystis, for which the names Thiocystis chemoclinalis sp. nov. and Thiocystis cadagnonensis sp. nov. are proposed, respectively. The type strains of T. chemoclinalis sp. nov. and T. cadagnonensis sp. nov. are CadH11T ( = JCM 15112T  = KCTC 5954T) and Cad448T ( = JCM 15111T  = KCTC 15001T), respectively.

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