PERMANOVA, ANOSIM, and the Mantel test in the face of heterogeneous dispersions: What null hypothesis are you testing?

Resilience of ecological communities to perturbation is important in the face of increased global change from anthropogenic stressors. Monitoring is required to detect the impact of, and recovery from, perturbations, and before-after-control-impact (BACI) analysis provides a powerful framework in this regard. However, species in a community are not observed with perfect detection, and occupancy analysis is required to correct for imperfect detectability of species. We present a Bayesian community occupancy before-after-control-impact (CO-BACI) framework to monitor ecological community response to perturbation when constituent species are imperfectly detected. We test the power of the model to detect changes in community composition following an acute perturbation with simulation. We then apply the model to a study of the impact of a large hurricane on the forest bird community of Sweden, using data from the national bird survey scheme. Although simulation shows the model can detect changes in community occupancy following an acute perturbation, application to a Swedish forest bird community following a major hurricane detected no change in community occupancy despite widespread forest loss. Birds with landscape occupancy less than 50% required correcting for detectability. We conclude that CO-BACI analysis is a useful tool that can incorporate rare species in analyses and detect occupancy changes in ecological communities following perturbation, but, because it does not include abundance, some impacts may be overlooked.

Understanding change in benthic marine systems.

Changes in ecological communities are often measured by the use of diversity or indices. Although many indices are available, their statistical properties are usually unknown and significance cannot be assigned to the value of a similarity index or to the difference between two values of a diversity index. FAUNSIM is a nonparametric method for determining the statistical significance of differences between two species assemblages for which no replicate samples are available. It makes use of Monte Carlo simulation and knowledge of the pool of species that may be found in the general region of interest. It generates an approximate probability distribution for the number-of species expected to be common to the two 888emblages of interest. This method was applied to trawl survey data from Samar Sea, the Philippines. Using FAUNSIM, significant differences in the assemblages of demersal fish were found in both time and space. Deep and shallow stations were occupied by distinct assemblages. Assemblages at some stations changed significantly froml979 to 1980. Visual inspection of changes in assemblages and standard diversity indices were not as effective as FAUNSIM in assessing the significance of observed changes in ecological communities.

Temporal changes in intertidal macrofauna communities over eight decades: A result of eutrophication and climate change

Interannual changes in the zooplankton community structure on the southeastern Bering Sea shelf during summers of 1994–2009

Microeukaryotic communities in intertidal sediments play an important role in maintaining ecosystem health and resilience, as they are involved in ecosystem services such as nutrient cycling, organic matter breakdown, and the support of diverse marine food webs. However, the seasonal variations in these communities and the differences between communities in muddy and sandy sediments are poorly understood. To address these gaps, surface sediments from both muddy and sandy sediments were collected monthly over a year (4 seasons, 10 months). Microeukaryotic community structure was analyzed using 18S rRNA sequencing, focusing on alpha-diversity, operational taxonomic unit composition, community composition, network structure, and trophic functional group structure. Results show that there were significant monthly changes in community composition, which were closely linked to changes in environmental factors such as temperature, dissolved oxygen (DO), and salinity. Species co-occurrence network analysis showed that interaction numbers and network density peaked in summer and declined in autumn and winter. This study also highlights the different characteristics of eukaryotic communities of muddy versus sandy sediments. Mantel tests show that temperature, DO, and chlorophyll a (chl a) have a significant influence on eukaryotic communities in muddy environments, while DO, chl a, and particulate organic carbon are important in sandy environments. It was found that autotrophs, heterotrophs, and mixotrophs react differently to seasonal climate shifts and different sediment types, with notable peaks in relative abundance for autotrophs in June, heterotrophs in December, and mixotrophs from September to November, as inferred from 18S rRNA amplicon sequencing data. These results will provide an important baseline on the microeukaryotic communities in intertidal sediments, essential for forecasting changes in community structure and ecosystem functions resulting from environmental changes.IMPORTANCEThis study is the first to report on dynamic changes in microeukaryotic operational taxonomic unit (OTU) composition in intertidal sediments, focusing on differences between muddy and sandy sediments over 10 months and across two different stations. A total of 4,452 OTUs were identified. Our findings offer new insights into how these communities are influenced by environmental factors, seasons, stations (Licun and Zhanqiao), and sediment types (sandy and muddy). Our results show significant monthly changes in community composition, closely linked to environmental factors such as temperature, dissolved oxygen, and salinity. The species co-occurrence network analysis revealed that interaction numbers and network density peaked in summer and declined in autumn and winter.

Microeukaryotic communities in intertidal sediments play an important role in maintaining ecosystem health and resilience, as they are involved in ecosystem services such as nutrient cycling, organic matter breakdown and the support of diverse marine food webs. However, the seasonal variations in these communities and the differences between communities in muddy and sandy sediments are poorly understood. To address these gaps, surface sediments from both muddy and sandy sediments were collected monthly over a year (4 seasons, 10 months). Microeukaryotic community structure was analyzed using 18S rRNA sequencing, focusing on alpha-diversity, OTU composition, community composition, network structure, and trophic functional group structure. Results show that there were significant monthly changes in community composition, which were closely linked to changes in environmental factors such as temperature, dissolved oxygen (DO) and salinity. Species co-occurrence network analysis showed that interaction numbers and network density peaked in summer and declined in autumn and winter. This study also highlights the different characteristics of eukaryotic communities of muddy versus sandy sediments. Mantel tests show that temperature, DO and chlorophyll a (chl a) have a significant influence on eukaryotic communities in muddy environments, while DO, chl a and particulate organic carbon (POC) are important in sandy environments. This suggests that eukaryotic communities in muddy sediments are susceptible to ocean warming and hypoxia, while those in sandy sediments are more vulnerable to hypoxia and pollution. It was also found that autotrophs, heterotrophs, and mixotrophs react differently to seasonal climate shifts and different sediment types, with notable peaks in abundance for autotrophs in June, heterotrophs in December, and mixotrophs from September to November. These results will provide an important baseline on the microeukaryotic communities in intertidal sediments, essential for forecasting changes in community structure and ecosystem functions resulting from environmental changes.

The pattern of changes in the macrobenthic community was studied along the south-east coast of India from the estuary to continental slope. A transect perpendicular to the coast was selected for sampling in estuary, inshore region, continental shelf and continental slope. Sampling was done in 16 stations in the depth range of 1.7–1000 m. The community structure was characterized in terms of species composition, abundance, diversity and feeding type. Four taxa were encountered in the study area comprising 181 species of polychaetes, 65 species of molluscs, 47 species of crustaceans and six species of ‘others’ (four echinoderms and two cnidarians). Polychaetes were found to be dominant at all the depths constituting 53.89% of the total abundance and 60.54% of the total number of species. Number of species and Shannon diversity of macrobenthos increased from estuary to shelf region and then decreased. The abundance was found to be maximum in the estuary and minimum in the slope. Carnivorous species were found to be dominant in the estuarine and inshore regions and surface deposit feeders in the shelf and slope regions. Dissolved oxygen decreased gradually from 30 m depth and beyond 150 m the decrease was pronounced due to the presence of the oxygen minimum zone. The distance based linear model (DISTLM) showed the environmental variables to explain about 76.45% of the total variability in macrofaunal distribution. Among the various environmental parameters, total organic carbon, depth and salinity explained more variability than others. Gradual change in community structure was quite evident with increase in depth.

Changes in the shelf macrobenthic community over large temporal and spatial scales in the Bohai Sea, China

Seasonal changes in the zooplankton community and population structure in the northern Bering Sea from June to September, 2017

Changes in macrobenthic communities were studied over a 3.5 yr period following restoration activities in Alewife Cove, a small estuary located in southeastern Connecticut, U.S. Development around this estuary had resulted in reduced freshwater and tidal inflows, loss of critical habitats such as salt marshes, and eutrophication. Early in 1988 the lower reach of the estuary was dredged to increase tidal flushing and enhance environmental quality. Following dredging, tidal range within the Cove increased from 52 to 83 cm. Due to erosion within the Cove's lower channel and sediment migration into the Cove, tidal flows and ranges approached pre-dredge levels by 1991. Despite these changes, the percentage of silt/clay in the surface sediments in the middle and upper basins of the Cove declined by 30–45% over the study period. Changes in infaunal community structure in the lower reach following dredging were not great, primarily comprising shifts in the relative abundances of species typical of sandier versus muddier sediments. Directional changes in community structure were most evident in the middle and upper basins, away from the dredged area. Infaunal species richness increased significantly, with many species previously found only in the sand habitats of the lower reach establishing populations in the middle and upper basins. There was a significant decrease in the summer abundances of the pollution indicator polychaeteCapitella capitata throughout much of the middle and upper basins. Restoration efforts in Alewife Cove centering on altered bydrology resulted in selected positive changes. Increases in tidal flow altered environmental conditons in the middle and upper basins where shifts in infaunal community structure indicated decreases in organic loading of sediments over 2–3 yr. Continued changes in the physical dynamics of the lower reach reduced tidal flow, arresting the positive ecological changes that were beginning to occur. This type of restoration approach of small estuaries can have positive results, but there may be a lag in the ecological response of the system. Macrobenthic communities, in particular summer abundance patterns of selected species, provided an integrated assessment of ecological changes in the Cove.

The present study focuses on the changes in sediment bacterial community structure and diversity of Sultanpur Lake due to changes in its hydrological regime. The assessment of the bacterial community structure was done by using the Next Generation Sequencing of 16S rRNA amplicon, a bacterial phylogenetic marker. Sultanpur Lake is located in Sultanpur National Park Gurugram, in the state of Haryana, India. This place harbors great plant and animal biodiversity and serves as an important feeding, roosting and breeding ground for both resident and migratory avian fauna. Increasing pollution level and scarcity of water during summer months impose a great threat to the lake. Sediment bacteria are considered as reliable recorders of nutrient cycling and active mediums of biogeochemical processes and thus were assessed in this study. Wet and dry sediment samples were taken and analyzed for their bacterial community structure and diversity. The amplicon sequencing generated 881,118 reads which corresponded to 93 known species in case of dry sediments and 8,71,102 reads corresponding to 44 species in case of wet sediments. In dry sediments the top ten phyla were Firmicutes (26%), Bacteroidetes (14%), Proteobacteria (15%), Cyanobacteria (12%), Parcubacteria (7%), Euryarcheota (6%), Actinobacteria (5%), Armatimonadetes (5%), Chloroflexi (2%) and Planctomycetes (2%). In case of wet sediments, the top ten phyla were Firmicutes (35%), Bacteroidetes (22%), Proteobacteria (22%), Actinobacteria (7%), Chloroflexi (5%) Parcubacteria (3%), Verrucomimicrobia (3%) and, Deinococcus-Thermus (3%). There was change in the community structure at species level too with Clostridium species as the most dominant species in case of wet sediments and Lactobacillus species as the predominant one in dry sediments. This study provides an insight into the changes in the bacterial communities due to changes in hydrology and how this change will affect the health of this wetland as irregular water supply is a major stressor of this wetland.

A study was conducted in 1986 and 1987 to determine the relationships between habitat characteristics and perturbation from insecticides on population and community dynamics of ground beetles collected with pitfall traps at 29 mixed-grass rangeland plots in northwestern South Dakota. Detrended correspondence analysis (DCA) and correlation analysis were used to define ecological gradients underlying changes in community structure of ground beetles. Results indicated that spatial changes in ground beetle communities occurred along gradients of percentage of clay, sand, and silt in soils and coverage of bare ground but were not related to vegetation. Twenty of the plots, located in two 1,400-ha blocks, were treated aerially with malathion liquid spray or carbaryl–bran bait in early July 1986. Pitfall trap catches of the dominant species declined significantly in one or both treatment blocks. However, catches rebounded to or above pretreatment levels a year after treatments. Results from DCA and multiple regression analysis of communities sampled in both years indicated that specific habitat characteristics were associated with immediate changes in community structure after perturbation; communities in habitats with high coverage of Buchloe dactyloides (Nutt.) Engelm., low coverage of Bouteloua gracilis (H.B.K.) Lag. ex Steud., and low clay soils were more resistant to change. Community malleability, or the tendency of communities to return to their predisturbed state, was not affected by treatment and was greater in habitats with high coverage of B. dactyloides and sedges and low coverage of B. gracilis and forbs. These variables are undoubtedly associated with other habitat characteristics as well.

A new index of dissimilarity is proposed to measure changes in community structure caused by environmental stress. A new statistical algorithm was also devised to test the similarity or dissimilarity between two communities. This procedure tests the mean dissimilarity within two communities against the mean dissimilarity between the same communities. These new indices are used along with other traditional indices of community structure in a proposed hierarchical scheme for testing different degrees of changes in stressed communities. Several examples illustrate that the procedures proposed give a more interpretible comprehensive analysis than the use of a limited set of indices.

Change in oceanographic conditions causes structural alterations in marine fish communities, but this effect may go undetected as most monitoring programs until recently mainly have focused on oceanography and commercial species rather than on whole ecosystems. In this paper, the objective is to describe the spatial and temporal changes in the Barents Sea fish community in the period 1992–2004 while taking into consideration the observed abundance and biodiversity patterns for all 82 observed fish species. We found that the spatial structure of the Barents Sea fish community was determined by abiotic factors such as temperature and depth. The observed species clustered into a deep assemblage, a warm water southern assemblage, both associated with Atlantic water, and a cold water north-eastern assemblage associated with mixed water. The latitude of the cold water NE and warm water S assemblages varied from year to year, but no obvious northward migration was observed over time. In the period 1996–1999 we observed a significant reduction in total fish biomass, abundance, mean fish weight, and a change in community structure including an increase in the pelagic/demersal ratio. This change in community structure is probably due to extremely cold conditions in 1996 impacting on a fish community exposed to historically high fishing rates. After 1999 the fish community variables such as biomass, abundance, mean weight, P/D ratio as well as community composition did not return to levels of the early 90s, although fishing pressure and climatic conditions returned to earlier levels.