Protein domain identification methods and online resources

Protein domains are the basic units of proteins that can fold, function, and evolve independently. Knowledge of protein domains is critical for protein classification, understanding their biological functions, annotating their evolutionary mechanisms and protein design. Thus, over the past two decades, a number of protein domain identification approaches have been developed, and a variety of protein domain databases have also been constructed. This review divides protein domain prediction methods into two categories, namely sequence-based and structure-based. These methods are introduced in detail, and their advantages and limitations are compared. Furthermore, this review also provides a comprehensive overview of popular online protein domain sequence and structure databases. Finally, we discuss potential improvements of these prediction methods.

The soil fauna of a beech forest on limestone: trophic structure and energy budget

The soil fauna of a mull beech forest on lime-stone in southern Lower Saxony (West Germany) was sampled quantitatively. Biomass estimates, trophic characteristics, and measurement and calculation of the energetic parameters of the constituent animal populations were used to construct an energy budget of the total heterotrophic subsystem of the forest. Mean annual zoomass amounted to about 15 g d wt m^-2; earthworms (about 10 g d wt m^-2) and other groups of the macrofauna were dominant. Protozoa constituted about 1.5 g d wt m^-2. Relative distribution of zoomass among the trophic categories was 50% macrosaprophages, 30% microsaprophages, 12% microphytophages, and 4% zoophages. Total annual consumption rate of the saprophagous and microphytophagous soil fauna (6328 and 4096 kJ m^-2 yr^-1, respectively) was of the same order of magnitude as annual litter fall (canopy leaves 6124 kJ m^-2 yr^-1, flowers and fruits 944 kJ m^-2 yr^-1, herbs 1839 kJ m^-2 yr^-1, fine woody material 870 kJ m^-2 yr^-1, tree roots 3404 kJ m^-2 yr^-1, without coarse woody litter). Primary decomposers (macrosaprophages) were the key group for litter comminution and translocation onto and into the soil, thus contributing to the high decomposition rate (k=0.8) for leaf litter. Consumption rates of the other trophic groups were (values as kJ m^-2 yr^-1): bacteriophages 2954, micromycophages 416, zoophages 153. Grazing pressure of macrophytophages (including rhizophages) was low. Faeces input from the canopy layer was not significant. Grazing pressure on soil microflora almost equalled microbial biomass; hence, a large fraction of microbial production is channelled into the animal component. Predator pressure on soil animals is high, as a comparison between consumption rates by zoophages and production by potential prey - mainly microsaprophages, microphytophages and zoophages - demonstrated. Soil animals contributed only about 11% to heterotrophic respiration. However, there is evidence that animals are important driving variables for matter and energy transfer: key processes are the transformation of dead organic material and grazing on the microflora. It is hypothesized that the soil macrosaprophages are donor-limited.

A global overview of the trophic structure within microbiomes across ecosystems

The colossal project of mapping the microbiome on Earth is rapidly advancing, with a focus on individual microbial groups. However, a global assessment of the associations between predatory protists and their bacterial prey is still missing at a cross-ecosystem level. This knowledge is critical to better understand the importance of top-down links in structuring microbiomes. Here, we examined 38 sequence-based datasets of paired bacterial and protistan taxa, covering 3,178 samples from diverse habitats including freshwater, marine and soils. We show that community profiles of protists and bacteria strongly correlated across and within habitats, with trophic microbiome structures fundamentally differing across habitats. Soils hosted the most heterogenous and diverse microbiomes. Protist communities were dominated by predators in soils and phototrophs in aquatic environments. This led to changes in the ratio of total protists to bacteria richness, which was highest in marine, while that of predatory protists to bacteria was highest in soils. Taxon richness and relative abundance of predatory protists positively correlated with bacterial richness in marine habitats. These links differed between soils, predatory protist richness and the relative abundance of predatory protists positively correlated with bacterial richness in forest and grassland soils, but not in agricultural soils. Our results suggested that anthropogenic pressure affects higher trophic levels more than lower ones leading to a decoupled trophic structure in microbiomes. Together, our cumulative overview of microbiome patterns of bacteria and protists at the global scale revealed major patterns and differences of the trophic structure of microbiomes across Earth's habitats, and show that anthropogenic factors might have negative effects on the trophic structure within microbiomes. Furthermore, the increased impact of anthropogenic factors on especially higher trophic levels suggests that often-observed reduced ecosystem functions in anthropogenic systems might be partly attributed to a reduction of trophic complexity.

When do evolutionary food web models generate complex networks?

Evolutionary foodweb models are used to build food webs by the repeated addition of new species. Population dynamics leads to the extinction or establishment of a newly added species, and possibly to the extinction of other species. The food web structure that emerges after some time is a highly nontrivial result of the evolutionary and dynamical rules. We investigate the evolutionary food web model introduced by Loeuille and Loreau (2005), which characterizes species by their body mass as the only evolving trait. Our goal is to find the reasons behind the model's remarkable robustness and its capability to generate various and stable networks. In contrast to other evolutionary food web models, this model requires neither adaptive foraging nor allometric scaling of metabolic rates with body mass in order to produce complex networks that do not eventually collapse to trivial structures. Our study shows that this is essentially due to the fact that the difference in niche value between predator and prey as well as the feeding range are constrained so that they remain within narrow limits under evolution. Furthermore, competition between similar species is sufficiently strong, so that a trophic level can accommodate several species. We discuss the implications of these findings and argue that the conditions that stabilize other evolutionary food web models have similar effects because they also prevent the occurrence of extreme specialists or extreme generalists that have in general a higher fitness than species with a moderate niche width.

Spatial variation in coral reef fish and benthic communities in the central Saudi Arabian Red Sea

Local-scale ecological information is critical as a sound basis for spatial management and conservation and as support for ongoing research in relatively unstudied areas. We conducted visual surveys of fish and benthic communities on nine reefs (3–24 km from shore) in the Thuwal area of the central Saudi Arabian Red Sea. Fish biomass increased with increasing distance from shore, but was generally low compared to reefs experiencing minimal human influence around the world. All reefs had a herbivore-dominated trophic structure and few top predators, such as sharks, jacks, or large groupers. Coral cover was considerably lower on inshore reefs, likely due to a 2010 bleaching event. Community analyses showed inshore reefs to be characterized by turf algae, slower-growing corals, lower herbivore diversity, and highly abundant turf-farming damselfishes. Offshore reefs had more planktivorous fishes, a more diverse herbivore assemblage, and faster-growing corals. All reefs appear to be impacted by overfishing, and inshore reefs seem more vulnerable to thermal bleaching. The study provides a description of the spatial variation in biomass and community structure in the central Saudi Arabian Red Sea and provides a basis for spatial prioritization and subsequent marine protected area design in Thuwal.

Trophic linkage of a temperate intertidal macrobenthic food web under opportunistic macroalgal blooms: A stable isotope approach

The effects of blooms of opportunistic green macroalgae, Ulva prolifera, on the trophic structure of the macrobenthic food web in a temperate intertidal zone on the western coast of Korea were evaluated using carbon and nitrogen stable isotopes. Biomasses of Ulva and microphytobenthos (MPB) increased significantly at the macroalgae-bloom and the non-bloom sites, respectively, from March to September 2011. The δ(13)C values of most the consumers were arrayed between those of MPB and Ulva at both sites, and differed according to feeding strategies at the macroalgae-bloom site. Seasonally increasing magnitudes in δ(13)C and δ(15)N values of consumers were much steeper at the macroalgae-bloom site than at the non-bloom site. Our findings provide evidence that blooming green macroalgae play a significant role as a basal resource supporting the intertidal macrobenthic food web and their significance varies with feeding strategies of consumers as well as the resource availability.

The diversity of soil mesofauna declines after bamboo invasion in subtropical China

Plant invasions often act as ecosystem 'simplifiers' to simplify diversity and community structure of soil biota. However, inconsistent relationships between plant invasion and soil fauna have been found and few studies have addressed how soil fauna communities change upon plant invasions across taxa and feeding guilds. Here, we investigated the effects of moso bamboo (Phyllostachys edulis) invasion in subtropical China on soil mesofauna communities using novel high-throughput sequencing (HTS). Specifically, we analyzed the spatio-temporal dynamics of fauna diversity and feeding guilds in the litter and soil layers for three stages of moso bamboo invasion, i.e., uninvaded (secondary broadleaved forest), moderately invaded (mixed bamboo forest) and completely invaded (P. edulis forest). Overall, we found that the completely invaded bamboo forest decreased species richness and diversity of total fauna, herbivores, and microbivores consistently across different soil layers, but less so detritivores and predators. Although we did not find any interaction effects of bamboo invasion and soil layers on soil fauna diversity indices, significant interaction effects were found on the community composition, for total fauna and their feeding guilds. Specifically, the detrimental effects of bamboo invasion on the trophic structure of soil fauna communities were more profound in the litter layer than in the soil layer, suggesting that a litter layer with more diverse taxa does not mean higher resistance to plant invasion in maintaining the soil food web structure. Taken together, our findings suggest that different responses within fauna feeding guilds to plant invasion were pervasive, and a deeper soil layer may better alleviate the negative effects of pant invasion on fauna community structure. These shifts in soil biodiversity may further degrade ecosystem functioning.

Do artificial structures cause shifts in epifaunal communities and trophic guilds across different spatial scales?

In the current frame of proliferation of artificial structures in the sea, the ecological effects of artificial substrates on marine environments and their associate biota become a topic of great scientific and conservationist interest. This study was focused on the amphipod communities from western Mediterranean Sea and tested, using the same secondary substrate, Ellisolandia elongata, if the community and trophic structure differ between artificial (two concrete-based: cubes and tetrapods, and one natural rock-based: rip-raps) and natural substrates. Results usually showed lower taxa number and diversity in artificial substrates, as well as differences in composition and trophic structure of the amphipod community. However, patterns were not consistent for all localities, evidencing the importance of local scale. Other potential factors, besides the substrate type, should be considered to understand particularities of each locality in management and conservation strategies.

Response of free-living marine nematodes to the southern Yellow Sea Cold Water Mass

The Yellow Sea Cold Water Mass is a remarkable seasonal hydrographic event in the bottom water of the Yellow Sea. In order to reveal the response of free-living marine nematodes to this event, community structure and biodiversity indices of nematodes were studied in June and November 2013. The dominant species were Dorylaimopsis rabalaisi, Spilophorella sp., Daptonema sp., Sabatieria sp. and Parasphaerolaimus sp. In terms of trophic structure, epigrowth feeders were the most dominant group. Correlation analysis showed that Shannon-Wiener diversity index had significantly negative correlation with sediment silt-clay percentage, organic matter content and water content. Results of BIOENV indicated that sediment phaeophorbide content, water content, bottom water salinity and temperature were the most important factors related to nematode community. In conclusion, community structure and biodiversity indices of nematodes were consistent in the two sampling seasons.

Comparative trophic structures of macrobenthic food web in two macrotidal wetlands with and without a dike on the temperate coast of Korea as revealed by stable isotopes

This study characterized trophic structures of the macrobenthic food webs in two contrasting estuarine wetlands, with and without a dike, on the southern coast of Korea, based on the δ¹³C and δ¹⁵N values of dominant macrobenthic consumers. The pelagic algal biomasses were similar in the upper Phragmites australis-covered and lower bare intertidal habitats partitioned by the dike, but the microphytobenthos (MPB) biomasses were extremely low in the Phragmites bed. The consumer δ¹³C values were more negative and their isotopic niche width was much narrower in the upper than in the lower habitat at the diked site. These dissimilar spatial patterns between sites suggest a simplified food-web structure, which reflects the reduced availability of MPB in the upper habitat in the dike-impacted site. Overall, our findings suggest that restriction of the tides by dike construction induces local changes in basal resource availability and faunal composition, leading to macrobenthic community trophic reorganization.

Coupling isotopic analysis and Ecopath model to detect the ecosystem features based on functional groups of the southwestern Yellow Sea, China

The paper evaluates the species richness, material transfer, energy flow, and system function of the southwestern Yellow Sea Ecosystem (SYSE) indicating intensive human intervention affecting this large marine ecosystem. Twenty functional groups were chosen to represent the basic components of the SYSE for Ecopath modeling based on offshore surveys, annual bird observations, and the China Fisheries Statistical Yearbooks. Forty-nine species based on 15 functional groups of Ecopath model were assessed by stable isotopic analysis (SIA) to verify ecosystem features, energy flow, and trophic structure of the SYSE derived from Ecopath model. Results showed there was a clear correlation of the estimated trophic structure calculated from SIA and the Ecopath model with R²=0.7184. The SYSE Ecopath model was still at an immature and unstable stage according to outputs of the modeling parameters. This paper provides a verification method of detecting the ecosystem features and maturity, stability, and resilience of marine ecosystems by comparing outputs from Ecopath models with SIA.

Trophic structure in a pilot system for the integrated multi-trophic aquaculture off the east coast of Korean peninsula as determined by stable isotopes

To assess the potential for nutritional exploitation of caged-fish-derived waste through the use of extractive co-cultured species in a pilot system for an integrated multi-trophic aquaculture (IMTA), we compared their C and N stable isotope ratios with those of uncultured macroinvertebrates in and around the system. Black rockfish were co-cultured with sea cucumber, oyster, and two macroalgae as extractive species. Isotope signatures of the co-cultured sea cucumber at the IMTA site differed from those at the control site, indicating their assimilation of aquaculture wastes. In contrast, δ(13)C and δ(15)N of individual taxa of the cultured oyster and uncultured invertebrates were consistent between sites, suggesting a minor contribution of the aquaculture waste to benthic and pelagic food chains in and around the IMTA system. These results provide evidence of the suitability of using sea cucumber as an extractive species to reduce the impact of a monoculture system on the ambient environment.

Effects of changes in isotopic baselines on the evaluation of food web structure using isotopic functional indices

Background

This study aimed to assess whether ecological inferences from isotopic functional indices (IFIs) are impacted by changes in isotopic baselines in aquatic food webs. We used sudden CO₂-outgassing and associated shifts in DIC-δ¹³C brought by waterfalls as an excellent natural experimental set-up to quantify impacts of changes in algal isotopic baselines on ecological inferences from IFIs.

Methods

Carbon (δ¹³C) and nitrogen (δ¹⁵N) stable isotopic ratios of invertebrate communities sharing similar structure were measured at above- and below-waterfall sampling sites from five rivers and streams in Southern Quebec (Canada). For each sampled invertebrate community, the six Laymans IFIs were then calculated in the δ -space (δ¹³C vs. δ¹⁵N).

Results

As expected, isotopic functional richness indices, measuring the overall extent of community trophic space, were strongly sensitive to changes in isotopic baselines unlike other IFIs. Indeed, other IFIs were calculated based on the distribution of species within δ-space and were not strongly impacted by changes in the vertical or horizontal distribution of specimens in the δ-space. Our results highlighted that IFIs exhibited different sensitivities to changes in isotopic baselines, leading to potential misinterpretations of IFIs in river studies where isotopic baselines generally show high temporal and spatial variabilities. The identification of isotopic baselines and their associated variability, and the use of independent trophic tracers to identify the actual energy pathways through food webs must be a prerequisite to IFIs-based studies to strengthen the reliability of ecological inferences of food web structural properties.

Incorporation of Cochlodinium bloom-derived organic matter into a temperate subtidal macrobenthic food web as traced by stable isotopes

Harmful algal blooms involving the dinoflagellate Cochlodinium polykrikoides occur every summer off the Korean peninsula's central southern coast. To determine whether Cochlodinium bloom-derived organic carbon is incorporated into the subtidal macrobenthic food web, we compared the δ¹³C and δ¹⁵N values of suspended particulate organic matter (SPOM) and sedimentary organic matter, and macrobenthic consumers between bloom and non-bloom seasons. Chemotaxonomic analysis revealed the presence of Cochlodinium blooms in summer and a predominance of diatoms in autumn. Both the δ¹³C and δ¹⁵N values of SPOM were higher in the bloom than in the non-bloom seasons. Such temporal shifts in the δ¹³C and δ¹⁵N values were also observed for most macrobenthic consumers collected in both seasons. Consistent temporal isotopic shifts in SPOM and macrobenthos revealed that the Cochlodinium bloom-derived carbon was incorporated into the coastal benthic food web, resulting from its increasing availability during blooms.

Effects of artificial reef and fishing moratorium on trophic structure of biological community in the Pearl River Estuary marine ranch based on stable isotopes

Deployment of artificial reefs (ARs) has become popular technique to create new hard-bottom habitats, increase biodiversity and richness for fisheries. We compared the faunal community structure and food web structure associated with before and after fishing moratorium between ARs and non-ARs in Wanshan Island, Pearl River Estuary using stable isotope techniques. Community composition showed higher differences between ARs and non-ARs. The range of δ13C and δ15N of different functional groups can distinguish the pelagic and benthic trophic pathways of the food web in reef-or-not area before and after fishing moratorium. The isotopic niches of entire faunal, as well as individual functional groups, overlapped less between ARs and non-ARs in Wanshan Island, which makes the isotopic functional indices non-equivalent. The total convex hull area (TA) of ARs was larger than that of non-ARs, indicating that nutrient pathways of ARs were more diverse. Overall, however, these results suggest that trophic structure was convergence between ARs and non-ARs, and differences before and after fishing moratorium, possibly due to seasonal differences. Finally, it was shown that the construction of ARs had a weak effect on the restoration of fishery resources in this area, which might be related to lack of further management, or even similar community composition to non-ARs areas.

Response of a seagrass fish assemblage to improved wastewater treatment

We compared the structure of a seagrass fish assemblage near a sewage outlet before and after improvements to wastewater treatment. To determine whether responses by the fish assemblage were due to changes in water quality or to other factors, comparisons were made with the structure of a fish assemblage from a nearby site unaffected by sewage effluent. Total species richness, density and biomass of fish, decreased at both sites over the 30-year period. An increase in mean trophic level near the sewage outlet following improvements in water quality indicated that wastewater treatment had another important effect. This result is consistent with the reductions in food webs supporting pelagic and benthic fishes that typically accompany decreases in nutrient inputs. Although improvements to wastewater treatment explained much of the variation in the structure of the fish assemblage at PC, our results also suggest that fishing and climate change, at both sites.

Trophic response of fishes to rainfall variability in a temperate estuarine system of Korea: A stable isotope approach

To assess the basal resources supporting food webs impacted by rainfalls, we compared stable isotope ratios (δ¹³C and δ¹⁵N) of fish consumers and organic matter sources between up- and down-sites in an estuary between seasons (June and September) and years (2018 and 2019) that showed different patterns of summer monsoon. Our study showed seasonal differences in the δ¹³C and δ¹⁵N values of basal resources and fish consumers in both years. At the up-site, significant differences of δ¹³C values of fish consumers were found between years, resulting from changing rainfall period, thereby causing a shift in food availability from terrigenous organic matter to periphyton. In contrast, at the down-site, the consistent isotopic values of fishes were observed in both years, suggesting that rainfall shift has a negligible impact on resources for fishes. Overall, the annual shift in resources for fishes in the estuary may be controlled by contrasting rainfall events.

Reef fish assemblages associated to new mat-forming zoantharian communities in the Canary Islands

Proliferations of zoantharians along tropical and subtropical regions are increasingly common and usually associated with anthropogenic impacts and ecosystem degradation. In the Canary Islands, we studied how the dominance in the substrate of Palythoa caribaeorum and Zoanthus pulchellus affected fish communities. For that purpose, we recorded the composition and biodiversity of fish assemblages associated to both zoantharian and macroalgae dominated habitats. In general terms, we found significant reductions of total fish abundance and richness at P. caribaeorum dominated habitats compared with macroalgae stands. However, in terms of trophic structure, there were significant changes within both zoantharian habitats depending on their coverages of the substrate. Herbivores and small invertebrate feeders, which are more adapted to forage in the macroalgae canopy, were less abundant in zoantharian habitats. This study demonstrates that the increasing dominance of zoantharians throughout the archipelago restructure the ecosystems and impact the native fish communities, that may offer a positive feedback for invasive tropical species to thrive.

Isotopic evidence for the dietary difference between Rhizostomeae Nemopilema nomurai and Semaeostomeae Cyanea nozakii

Blooms of the Rhizostomeae Nemopilema nomurai and the Semaeostomeae Cyanea nozakii have become more prominent in the coastal waters of China since the end of the 20th century. However, the trophic ecology of these jellyfish species remain incompletely understood. In this study, the trophic characterizations of N. nomurai and C. nozakii populations were assessed using stable isotope analysis (SIA), with a focus on the important bloom area offshore of the Yangtze Estuary. Our results indicated obvious trophic differences between two scyphomedusae. The higher trophic position of the C. nozakii population in the coastal planktonic food web was reflected by its relatively large δ15N value compared to that of N. nomurai. The MixSIAR model indicated that small copepods (<1000 μm) and seston were important food sources for N. nomurai, and showed a stable dietary, irrespective of N. nomurai size. Conversely, C. nozakii exhibited a more diverse diet composition, and gelatinous organisms also were an important part of the diet of C. nozakii. Moreover, a pronounced ontogenetic shift in the diet of C. nozakii was observed, consisting of an increase in the proportion of zooplanktonic prey (excluding seston) in the C. nozakii diet with diameter. This study provides isotopic evidence of the substantial difference in trophic ecology between N. nomurai and C. nozakii, which resulted from the variations in SI values and diet compositions. Inconsistent size-based variation patterns were observed in trophic ontogenetic shifts within the N. nomurai and C. nozakii groups, highlighting a need for further investigation. These results will give insights into the characteristics of trophic ecology and functional roles of Rhizostomeae and Semaeostomeae, and indicate the need for a more careful consideration of the representations of Rhizostomeae and Semaeostomeae in coastal ecosystems, so as not to underestimate the knowledge of taxon-specific ecological effects on energy flow.

Assessing lake ecological status across a trophic gradient through environmental and biological variables

The Water Framework Directive was widely welcomed because it sought to integrate chemical and biological elements of aquatic ecosystems to achieve 'good ecological status', reflecting at most slight anthropogenic impact. However, implementation has been criticised because of the failure to adequately integrate these elements and assess status of the whole ecosystem. In this study, a suite of environmental and biotic variables was measured to assess their relative importance as predictors of lake status for 50 lakes in the north of the island of Ireland. Total Phosphorus (TP) had a strong effect on taxon biomasses and ecological quality ratios (EQR) for most taxa, as expected, but other environmental variables, such as pH, water colour and spatial location, were also important. Most variance in mean EQR, the average of the taxon values, was predicted by five environmental variables (chlorophyll a, TP, population density, water colour and elevation) and whether (alien) cyprinid fish were present. Oligotrophic lakes with cyprinid fish had lower mean EQRs than cyprinid-free lakes, indicating the importance of recording species introductions when assessing lake status. Strong evidence for bottom-up effects was also detected, and cyprinids probably influenced trophic structure by increasing nutrient release from the sediment rather than by top-down effects. Phytoplankton biomass, fish biomasses, and the percentage of predatory fish, increased with TP. Our results further emphasize the need to adopt a more integrated approach when assessing lake status.

Trophic structure and origin of resources of soil macrofauna in the salt marsh of the Wadden Sea: a stable isotope (15N, 13C) study

Salt marshes exist along the gradient of the marine mudflat to the terrestrial dunes, with a gradient of shore height and associated plant zonation. The lower salt marsh (LSM) extends from the mean high tidal level to 35 cm above that level and is followed by the upper salt marsh (USM). Despite changes in the amount of allochthonous marine input and in abiotic conditions, little is known about changes in the trophic structure and used of basal resources by the soil macrofauna along marine-terrestrial boundaries. Natural variations in carbon stable isotope ratios (δ13C signatures) allow insight into basal resources of consumers such as marine algae, terrestrial C3 and C4 photosynthesising plants. Furthermore, variations in nitrogen stable isotope ratios (δ15N signatures) allow insight into the trophic position of consumers. We investigated spatial and temporal changes in stable isotope signatures in salt marsh soil macrofauna of the island of Spiekeroog, German Wadden Sea. The range of δ15N signatures indicated no changes in food chain length across salt marsh zones with consumers in both zones comprising primary decomposers, secondary decomposers and first order predators. However, the trophic position of individual species changed between zones, but in particular with season. Contrasting δ15N signatures, the range in δ13C signatures in the LSM was twice that in the USM indicating a wider range of resources consumed. Bayesian mixing models indicated predominant autochthonous resource use in both the LSM and USM, with the use of marine allochthonous resources never exceeding 29.6%. However, the models also indicate an increase in the use of marine resources in certain species in the LSM with no use in the USM. Overall, the results indicate that the resource use of salt marsh macrofauna varies more in space than in time, with the food web being generally based on autochthonous rather than allochthonous resources. However, there also is trophic plasticity in certain species across both temporal and spatial scales including variations in the use of allochthonous resources. Generally, however, marine input contributes little to the nutrition of salt marsh soil macroinvertebrates.

Energy flow analysis of grass carp pond system based on Ecopath model

Grass carp (Ctenopharyngodon idellus) is the most productive freshwater fish in China, but its traditional aquaculture model still has problems, such as poor water quality and frequent diseases. We have taken monoculture and 80:20 polyculture grass carp ponds as the research object and used EwE software to build the Ecopath model of two ponds. We analyzed and compared the characteristics of ecological structure and energy flow in two ponds. The result showed the highest effective trophic level in the polyculture pond that was higher than that in the monoculture pond, and fish in polyculture had higher EE values which showed the production of fish in polyculture contributed more to the energy conversion efficiency of the ecosystem. Flows into detritus were the largest component of TST both in the two ponds, which accounted for 49.34% and 50.37%. And the average transfer efficiency in monoculture was 13.07%, while that in polyculture was 15.6%. The ascendency/total development capacity (A/TDC) and overhead/total development capacity (O/TDC) were 0.35 and 0.65 both in the two ponds, respectively, which indicated that both systems had a strong anti-perturbation ability, but the stability could be improved. Finn's cycling index (FCI) in polyculture was higher and showed that the polyculture pond was more mature and stable. Unused energy of functional groups will flow to detritus, and that in the monoculture pond was higher, the energy of C. idellus that flowed to detritus in monoculture was 48.17% higher than that in polyculture; unused energy of bacteria and phytoplankton were also high. The result showed that polyculture could improve energy utilization, increase transfer efficiency, and raise the stability of the ecosystem. Grass carp ponds still need to be improved in the aspects of mixed species and energy consumption. It is necessary to improve the ecological and economic benefits of grass carp ponds by optimizing the aquaculture structure and adjusting the aquaculture proportion.

Marine toxin domoic acid alters protistan community structure and assembly process in sediments

Domoic acid (DA)-producing algal blooms have been the issue of worldwide concerns in recent decades, but there has never been any attempt to investigate the effects of DA on microbial ecology in marine environments. Protists are considered to be key regulators of microbial activity, community structure and evolution, we therefore explore the effect of DA on the ecology of protists via metagenome in this work. The results indicate that trace amounts of DA can act as a stressor to alter alpha and beta diversity of protistan community. Among trophic functional groups, consumers and phototrophs are negative responders of DA, implying DA is potentially capable of functional-level effects in the ocean. Moreover, microecological theory reveals that induction of DA increases the role of deterministic processes in microbial community assembly, thus altering the biotic relationships and successional processes in symbiotic patterns. Finally, we demonstrate that the mechanism by which DA shapes protistan ecological network is by acting on phototrophs, which triggers cascading effects in networks and eventually leading to shifts in ecological succession of protists. Overall, our results present the first perspective regarding the effects of DA on marine microbial ecology, which will supplement timely information on the ecological impacts of DA in the ocean.

Ecological habitat quality assessment of a tropical estuary using macrobenthic functional characteristics and biotic indices

Seasonal variation in the macrobenthic functional characteristics, such as trophic structure and secondary production, was studied, along with their structural characteristics such as density, biomass, and community distribution in Cochin estuary (CE), a tropical monsoonal estuary along the Southwest coast of India during 2018-2019. The biotic indices, AMBI (AZTI's Marine Biotic Index) and M-AMBI (Multivariate-AMBI) were used to assess the ecological quality of the study area by using the sensitivity of macrobenthic fauna to disturbances. A distinct temporal variation was evident in the macrobenthic structural characteristics, wherein high density, biomass, and species richness were observed during the post-monsoon. Polycheate species were dominant during pre-monsoon (Prionospio cirrifera) and monsoon (Mediomastus sp.), while gastropod species, Stenothyra perpumila, was dominant during post-monsoon. The trophic structure analysis revealed the dominance of deposit-feeding polychaetes during the pre-monsoon in association with the fine sediments laden with high organic carbon. In contrast, during post-monsoon, the polychaete trophic groups were more or less evenly distributed in the sandy substratum. The higher density of suspension feeders and herbivorous-grazers observed during the post-monsoon indicated improved habitat quality compared to the pre-monsoon dominated by the detritivores. The macrobenthic secondary production was also high during the post-monsoon, contributed by a diverse assemblage of molluscs, crustaceans, and polychaetes having size > 0.7 mm. The biotic indices also showed an evident increase in the habitat quality of the estuary from pre-monsoon to post-monsoon (AMBI, moderately disturbed to undisturbed; M-AMBI, poor-moderate-good to good-high conditions), similar to the results of benthic structural and functional characteristics. The study highlights the significance of the utility of benthic functional characteristics while assessing the habitat quality of an ecosystem.

Trophic niche overlap in coralline algae- and coral-dominated rocky-bottom subtidal communities

We investigated trophic structures in rocky subtidal ecosystems transitioning from canopy-forming to barren states across coastlines with varying oceanographic conditions. We examined stable isotopes and functional traits of common invertebrate and fish taxa to understand the food-web consequences. We hypothesized that resource exploitation patterns of functional guilds would result in distinct isotopic niches, defining trophic diversity and niche. δ13C and δ15N ranges of invertebrate functional groups differentiated pelagic from benthic trophic pathways, reflecting flexible dietary use in the absence of macroalgae. Fish production relied on prey using pelagic and benthic basal resources. Trophic redundancy among consumers within functional guilds contributed to intrinsic trophic structure in barren ecosystems. The resulting community-wide trophic diversity has led to consistent niche widths and overlapping niche space. Overall, our findings highlight the crucial roles of consumers that persist with diverse functional guilds in conferring the adaptability of barren rocky ecosystems following habitat disturbance.