Colonization patterns of stream benthos on artificial substrates in Taiwan

Experiments on the colonization of artificial substrates by stream benthos were conducted in upper Chingmei Stream, Taiwan. The artificial substrates were colonized by stream benthos for periods of 3, 6 12, 21, 30 and 42 days.The two experiments were designed for different purposes. Experiment I from December 15, 1990 to January 29, 1991 investigated the colonization patterns of stream benthos at two sites: a polluted site caused by coal mining activities (Site 1) and a recovery site further downstream of the polluted site (Site 2). Experiment II from March 14, 1991 to April 28, 1991 tested the effect of two different sizes of substrate (cobble and gravel) on the colonization patterns of stream benthos at Site 2. In Experiment I, the total number of individuals and taxa were significantly affected by exposure period of experimental substrates and sites which indicate the occurrence of succession and the detrimental effect of coal mining activities on the benthic community. At Site 1, only Caenis sp., Euphaea sp. and Chironomidae occurred on all sampling dates and were abundant. The other taxa may just continue to drift away from the site. The chironomid larvae were most abundant. They accounted for over 90% of the colonizing individuals from day 12 to day 42. At Site 2, Baetis spA and Chironomidae were most abundant. They accounted for over 80% during the experiment, except on day 21. The relative abundance shifted from Baetis sp.A to Chironomidae with an increase in colonization time. Association analysis was performed on the abundance of taxa pairs within the same functional feeding group at Site 2. The results suggest that filter-feeders and predators have concordant colonization patterns. The relationship between taxa and abundance at the two sites also was tested by lognormal distribution to determine the degree of equilibrium of the community. In Experiment II, the substratum types influenced only the total number of individuals colonizing baskets. The gravel substrate provides more surface area for stream benthos and supports more individuals. Baetis sp.A and chironomid larvae were abundant; they accounted for over 84% of the individuals from day 6 to 42 on both gravel and cobble. The chironomid larvae comprised 36% of the fauna on the gravel substrate and 35 - 79% of the fauna on the cobble substrate. The results of association analysis on the abundance of taxa pairs within the same functional feeding group showed that there were more taxa pairs with significant associations on cobble than on gravel. The negatively significant associations also occurred more on the cobble substrate. This indicates that biological interactions may be important in determining the development of community on the cobble substrate. Disturbance caused by floods influenced the colonization patterns, especially on the gravel substrate. It reset the artificial substrates back to earlier conditions. This study only suggests that competition may occur in the subtropical Taiwanese stream and further experimentation is needed to demonstrate whether competition occurs

Developing a biotic index for Colorado stream quality

November 1994.Also listed online under Open file reports list as no. 8.Includes bibliographical references (pages 114-118).Financed in part by the U.S. Dept. of the Interior, Geological Survey, grant no. 14-08-0001-G2008/3 11

A global database for metacommunity ecology, integrating species, traits, environment and space

The use of functional information in the form of species traits plays an important role in explaining biodiversity patterns and responses to environmental changes. Although relationships between species composition, their traits, and the environment have been extensively studied on a case-by-case basis, results are variable, and it remains unclear how generalizable these relationships are across ecosystems, taxa and spatial scales. To address this gap, we collated 80 datasets from trait-based studies into a global database for metaCommunity Ecology: Species, Traits, Environment and Space; “CESTES”. Each dataset includes four matrices: species community abundances or presences/absences across multiple sites, species trait information, environmental variables and spatial coordinates of the sampling sites. The CESTES database is a live database: it will be maintained and expanded in the future as new datasets become available. By its harmonized structure, and the diversity of ecosystem types, taxonomic groups, and spatial scales it covers, the CESTES database provides an important opportunity for synthetic trait-based research in community ecology

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure fl ux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defi ned as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium ) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the fi eld understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation it is imperative to delete or knock down more than one autophagy-related gene. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways so not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field

Macroinvertebrate assemblage patterns as indicators of water quality in the Xindian watershed, Taiwan

In the present study, we assessed the water quality along a stretch of the watershed with considerable economic importance at the Xindian in Taiwan, using macroinvertebrate assemblages, along with environmental variables. The research was carried out at the seven sampling sites (abbreviated as XD1-XD7) where human impacts varied in intensity from upstream tributaries to the downstream of the Xindian watershed from December 2010 to December 2011. All variables except for the hardness, pH, dissolved oxygen, conductivity, turbidity, phosphate, ammonia, and alkalinity were significantly different (P b 0.05) between the sampling sites. A total of seventy seven taxa belonging to forty five families within eight insect orders, along with three non-insect invertebrate taxa were recorded, with most representative orders being Ephemeroptera and Diptera. Mean values of the density, abundance of macroinvertebrates, Shannon index, Simpson index, and Pielou's evenness were much higher in the reference sites, XD2, XD3, and XD4 compared with impacted sites, XD5, XD6, and XD7. Most of the benthic metrics were greatest in the reference site compared to the impacted site. Only the composition measures, percentages of Chironomidae and Oligochaeta which are more tolerant to pollution were dominant in the impacted site, XD7. As the results of assessment by different benthic metrics, water quality of Xindian watershed became gradually worse from upstream to downstream. Generally, our results suggest that macroinvertebrate assemblages can be used for assessment of water quality

CESTES - A global database for metaCommunity Ecology: Species, Traits, Environment and Space

CESTES is a global database for metaCommunity Ecology: Species, Traits, Environment and Space. It compiles 80 datasets from trait-based studies. Each dataset includes four matrices: species community abundances or presences/absences across multiple sites, species trait information, environmental variables and spatial coordinates of the sampling sites. CESTES presents a harmonized structure and covers a diversity of ecosystem types (marine, terrestrial, freshwater), taxonomic groups (plants, vertebrates, invertebrates...), geographical regions, and spatial scales. The CESTES database is a live database: it will be maintained and expanded in the future as new datasets become available (https://icestes.github.io/sharedata). A zipped folder called “CESTES.zip” includes two alternative formats for the CESTES database: - a “xCESTES” folder that includes 80 Excel files (one file per dataset), each named according to the following structure: “AuthorPublicationYear.xlsx” - a “rCESTES” folder that includes the CESTES core processed database (comm, traits, envir, coord matrices) as an R list object “CESTES.RData” plus two R scripts, and two metadata tables for data processing and exploration. This “CESTES.zip” folder also includes: - an extended metadata table, “CESTES_metadata.xlsx”, that provides the general metadata information of all the datasets, - a tutorial document, “HOW_TO_SHARE_MY_DATA_FOR_CESTES.pdf”, that explains how to share data for integrating future datasets in the database. A second zipped folder, called "ceste.zip", corresponds to the non-spatial ancillary to CESTES. We provide access to 10 additional datasets that were not completely suitable for the CESTES database, due to the absence of spatial information or insufficient metadata but that were potentially valuable for their three other data matrices (comm, traits, envir). They follow the same structure as CESTES, except that they do not present the “coord” sheet and sometimes include only partial metadata. The “ceste.zip” zipped folder includes the 10 data files + 1 metadata file called "ceste_metadata.xlsx"

Author Correction: A global database for metacommunity ecology, integrating species, traits, environment and space

An amendment to this paper has been published and can be accessed via a link at the top of the paper