scholarly journals From Water into Sediment—Tracing Freshwater Cyanobacteria via DNA Analyses

2021 ◽  
Vol 9 (8) ◽  
pp. 1778
Author(s):  
Ebuka Canisius Nwosu ◽  
Patricia Roeser ◽  
Sizhong Yang ◽  
Lars Ganzert ◽  
Olaf Dellwig ◽  
...  
Keyword(s):  
Water Column ◽  
High Throughput Sequencing ◽  
Surface Sediments ◽  
Environmental Changes ◽  
Sediment Traps ◽  
Sequence Variant ◽  
Sediment Record ◽  
Term Monitoring ◽  
Taphonomic Processes

Sedimentary ancient DNA-based studies have been used to probe centuries of climate and environmental changes and how they affected cyanobacterial assemblages in temperate lakes. Due to cyanobacteria containing potential bloom-forming and toxin-producing taxa, their approximate reconstruction from sediments is crucial, especially in lakes lacking long-term monitoring data. To extend the resolution of sediment record interpretation, we used high-throughput sequencing, amplicon sequence variant (ASV) analysis, and quantitative PCR to compare pelagic cyanobacterial composition to that in sediment traps (collected monthly) and surface sediments in Lake Tiefer See. Cyanobacterial composition, species richness, and evenness was not significantly different among the pelagic depths, sediment traps and surface sediments (p > 0.05), indicating that the cyanobacteria in the sediments reflected the cyanobacterial assemblage in the water column. However, total cyanobacterial abundances (qPCR) decreased from the metalimnion down the water column. The aggregate-forming (Aphanizomenon) and colony-forming taxa (Snowella) showed pronounced sedimentation. In contrast, Planktothrix was only very poorly represented in sediment traps (meta- and hypolimnion) and surface sediments, despite its highest relative abundance at the thermocline (10 m water depth) during periods of lake stratification (May–October). We conclude that this skewed representation in taxonomic abundances reflects taphonomic processes, which should be considered in future DNA-based paleolimnological investigations.

Mapping and monitoring intertidal benthic habitats: a review of techniques and a proposal for a new visual methodology for the European coasts

2009 ◽  
Vol 33 (3) ◽  
pp. 378-402 ◽  
Author(s):  
Laurent Godet ◽  
Jérôme Fournier ◽  
Nicolas Toupoint ◽  
Frédéric Olivier
Keyword(s):  
Environmental Changes ◽  
Coastal Zones ◽  
Quick Method ◽  
Simple Method ◽  
Long Term Monitoring ◽  
Intertidal Habitats ◽  
Global Environmental Changes ◽  
Remote Sensing Methods ◽  
Term Monitoring

Mapping seafloors is a fundamental step for managing and preserving coastal zones. Moreover, in a context of current global environmental changes, new methods allowing long-term monitoring are increasingly required. Various methods have been used to map seafloors, primarily benthic macrofauna and sediment sampling along regular grids or transects, and remote sensing methods. These methods map very different things, do not have the same accuracy levels, and have different costs in time and money. Furthermore, such methods often require the competencies of highly skilled scientists and exclude non-specialists otherwise best placed to perform them. In this paper, we test a method based on Direct Field Observations (‘DFO method’), which can be used by non-specialists, and assess if it is sufficient for mapping and monitoring intertidal habitats. We further compare this method with other conventional ones. The results show that such a simple method is relatively rapid and inexpensive given the results obtained. Moreover, it is particularly suitable for highly fragmented intertidal landscapes where other methods are often very limited. In consequence, in areas such as the European coasts, it can be used by non-specialists, such as protected-area managers, and because it is an inexpensive and quick method long-term monitoring is also possible.

scholarly journals Contrasting vertical distributions of recent planktic foraminifera off Indonesia during the southeast monsoon: implications for paleoceanographic reconstructions

2022 ◽  
Author(s):  
Raúl Tapia ◽  
Sze Ling Ho ◽  
Hui-Yu Wang ◽  
Jeroen Groeneveld ◽  
Mahyar Mohtadi
Keyword(s):  
Vertical Distribution ◽  
Water Column ◽  
Surface Sediments ◽  
Tropical Indian Ocean ◽  
Distribution Patterns ◽  
Sediment Traps ◽  
Published Data ◽  
Foraminiferal Assemblage ◽  
Planktic Foraminifera ◽  
Neogloboquadrina Dutertrei

Abstract. Planktic foraminifera are widely used in palaeoceanographic and paleoclimatic studies. The accuracy of such reconstructions depends on our understanding of the organisms’ ecology. Here we report on field observations of planktic foraminiferal abundances (>150 µm) from 5 depth intervals between 0–500 m water depth at 37 sites in the eastern tropical Indian Ocean. The total planktic foraminiferal assemblage comprises 29 morphospecies; with 11 morphospecies accounting for ~90 % of the total assemblage. Both species composition and dominance in the net samples are broadly consistent with the published data from the corresponding surface sediments. The abundance and vertical distribution of planktic foraminifera are low offshore west Sumatra, and increase towards offshore south Java and the Lesser Sunda Islands (LSI). Average living depth of Trilobatus trilobus, Globigerinoides ruber, and Globigerina bulloides increases eastward, while that of Neogloboquadrina dutertrei, Pulleniatina obliquiloculata, and Globorotalia menardii remains constant. We interpret the overall zonal and vertical distribution patterns in planktic foraminiferal abundances as a response to the contrasting upper water column conditions during the southeast monsoon, i.e., oligotrophic and stratified offshore Sumatra (non-upwelling) vs. eutrophic and well-mixed offshore Java-LSI (upwelling). Overall, the inferred habitat depths of selected planktic foraminifera species show a good agreement with those from sediment trap samples and from surface sedimentss off Sumatra, but not with those from surface sediments off Java-LSI. The discrepancy might stem from the different temporal coverage of these sample types. Our findings highlight the need to consider how foraminiferal assemblages and ecology vary on shorter timescales, i.e., from “snapshots” of the water column captured by plankton net to seasonal and interannual variability as recorded in sediment traps and how these changes are transferred and preserved in deep-sea sediments.

scholarly journals Updating salamander datasets with phenotypic and stomach content information for two mainland Speleomantes

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Enrico Lunghi ◽  
Fabio Cianferoni ◽  
Simone Giachello ◽  
Yahui Zhao ◽  
Raoul Manenti ◽  
...  
Keyword(s):  
Environmental Changes ◽  
Stomach Contents ◽  
Phenotypic Traits ◽  
Large Dataset ◽  
Amphibian Species ◽  
Plethodontid Salamanders ◽  
Content Information ◽  
Term Monitoring ◽  
Long Term Studies

AbstractEuropean plethodontid salamanders (genus Speleomantes; formerly Hydromantes) are a group of eight strictly protected amphibian species which are sensitive to human-induced environmental changes. Long-term monitoring is highly recommended to evaluate their status and to assess potential threats. Here we used two low-impact methodologies to build up a large dataset on two mainland Speleomantes species (S. strinatii and S. ambrosii), which represents an update to two previously published datasets, but also includes several new populations. Specifically, we provide a set of 851 high quality images and a table gathering stomach contents recognized from 560 salamanders. This dataset offers the opportunity to analyse phenotypic traits and stomach contents of eight populations belonging to two Speleomantes species. Furthermore, the data collection performed over different periods allows to expand the potential analyses through a wide temporal scale, allowing long-term studies.

scholarly journals A metabarcoding comparison of taxonomic richness and composition between the water column and the benthic boundary layer

2020 ◽  
Author(s):  
H E Parry ◽  
A Atkinson ◽  
P J Somerfield ◽  
P K Lindeque
Keyword(s):  
Boundary Layer ◽  
Water Column ◽  
Benthic Boundary Layer ◽  
Monitoring Site ◽  
Benthic Assemblages ◽  
Low Light ◽  
Operational Taxonomic Units ◽  
Shelf Seas ◽  
Term Monitoring

Abstract Zooplankton monitoring in shelf seas predominantly uses nets that miss the benthic boundary layer (BBL) just above the seabed. However, this boundary between pelagic and benthic assemblages can be faunistically rich, having its own distinct hyperbenthic fauna and acting as a low-light refuge for overwintering or dielly migrating zooplankton. To compare species richness and composition between pelagic and BBL habitats, we sampled a long-term monitoring site in the Western English Channel seasonally. Metabarcoding methods applied to vertical net samples (top 50 m in a ∼54-m water column) and those from a hyperbenthic sledge generated >100 000 sequences clustered into 294 operational taxonomic units. Of these, 215 were found in the BBL and 170 in the water column. Some key taxa (e.g. mysids) were native to the BBL; by contrast, other delicate taxa (e.g. ctenophores) seemed to avoid the BBL. The major contrasts in plankton composition related to the seasonal cycle rather than to pelagic-BBL differences, suggesting that the basic dynamics of the site are captured by our ongoing long-term weekly resolution monitoring. Overall, metabarcoding approaches, applied to both water column and BBL, provide an independent view of plankton dynamics, and augment existing traditional methods.

scholarly journals LONG-TERM MONITORING OF ENVIRONMENTAL CHANGES ALONG CHINA-EUROPE RAILWAY EXPRESS (CER EXPRESS) USING MULTI-SOURCE REMOTELY SENSED DATA

2021 ◽  
Vol XLIII-B3-2021 ◽  
pp. 817-822
Author(s):  
B. Ma ◽  
X. Guo ◽  
J. Jiang ◽  
D. Culibrk ◽  
S. Ding ◽  
...  
Keyword(s):  
Environmental Degradation ◽  
Small Area ◽  
Environmental Changes ◽  
Comprehensive Evaluation ◽  
Environmental Indicators ◽  
Remotely Sensed Data ◽  
Ecological Changes ◽  
Long Term Monitoring ◽  
Term Monitoring

Abstract. The China-Europe Railway Express (CER-Express), not only promoted the cooperation between countries and regions across Asia and Europe but also gave rise to remarkable changes in landcover and had a profound effect on the natural environment along the railway in recent years. Effective ways to monitor and assess ecological changes are urgently needed to ensure sustainable development of CER-Express. There are very few existing environmental monitoring studies focusing on the area along the CERExpress. In this paper, we present a study of environmental degradation, which occurred during the construction and operation of CER-Express from 2010 to 2018, based on a comprehensive evaluation index (CEI), which takes three environmental indicators into account and provides a timely and reliable evaluation of environmental changes at large scales. In addition, the environment conditions of the regions and countries along the CER-Express have been quantified and comparatively studied at different scales over different periods, using histograms of mean CEI values. Furthermore, specific causes of environmental degradation in the rail-intensive countries and small-area countries along the railway are discussed. Our results show that the environmental degradation can be detected in most of the rail-intensive countries, such as Germany, Poland, Austria, and Czech Republic along the railway. Therefore, to ensure sustainability of the CER-Express, environmental protection along the railway should be paid more attention to and a reasonable arrangement for the exploitation of CER-Express devised.

scholarly journals Long-Term Adaptation of Acidophilic Archaeal Ammonia Oxidisers Following Different Soil Fertilisation Histories

2021 ◽  
Author(s):  
Jun Zhao ◽  
Baozhan Wang ◽  
Xue Zhou ◽  
Mohammad Saiful Alam ◽  
Jianbo Fan ◽  
...  
Keyword(s):  
Community Composition ◽  
High Throughput Sequencing ◽  
Environmental Changes ◽  
Agricultural Soils ◽  
Terrestrial Ecosystems ◽  
Low Ph ◽  
Ph Change ◽  
Monooxygenase Gene ◽  
Ammonia Oxidising Archaea

AbstractAmmonia oxidising archaea (AOA) are ecologically important nitrifiers in acidic agricultural soils. Two AOA phylogenetic clades, belonging to order-level lineages of Nitrososphaerales (clade C11; also classified as NS-Gamma-2.3.2) and family-level lineage of Candidatus Nitrosotaleaceae (clade C14; NT-Alpha-1.1.1), usually dominate AOA population in low pH soils. This study aimed to investigate the effect of different fertilisation histories on community composition and activity of acidophilic AOA in soils. High-throughput sequencing of ammonia monooxygenase gene (amoA) was performed on six low pH agricultural plots originating from the same soil but amended with different types of fertilisers for over 20 years and nitrification rates in those soils were measured. In these fertilised acidic soils, nitrification was likely dominated by Nitrososphaerales AOA and ammonia-oxidising bacteria, while Ca. Nitrosotaleaceae AOA activity was non-significant. Within Nitrososphaerales AOA, community composition differed based on the fertilisation history, with Nitrososphaerales C11 only representing a low proportion of the community. This study revealed that long-term soil fertilisation selects for different acidophilic nitrifier communities, potentially through soil pH change or through direct effect of nitrogen, potassium and phosphorus. Comparative community composition among the differently fertilised soils also highlighted the existence of AOA phylotypes with different levels of stability to environmental changes, contributing to the understanding of high AOA diversity maintenance in terrestrial ecosystems.

Temporal changes in cladoceran assemblages subjected to a low calcium environment: combining the sediment record with long-term monitoring data

Hydrobiologia ◽  
2016 ◽  
Vol 776 (1) ◽  
pp. 85-97 ◽  
Author(s):  
Laura E. Redmond ◽  
Adam Jeziorski ◽  
Andrew M. Paterson ◽  
James A. Rusak ◽  
John P. Smol
Keyword(s):  
Temporal Changes ◽  
Monitoring Data ◽  
Sediment Record ◽  
Low Calcium ◽  
Long Term Monitoring ◽  
Term Monitoring
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