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Although cannibalism is ubiquitous in food webs and frequent in systems where a predator and its prey also share a common resource (intraguild predation, IGP), its impacts on species interactions and the dynamics and structure of communities are still poorly understood. In addition, the few existing studies on cannibalism have generally focused on cannibalism in the top-predator, ignoring that it is frequent at intermediate trophic levels. A set of structured models shows that cannibalism can completely alter the dynamics and structure of three-species IGP systems depending on the trophic position where cannibalism occurs. Contrary to the expectations of simple models, the IG predator can exploit the resources more efficiently when it is cannibalistic, enabling the predator to persist at lower resource densities than the IG prey. Cannibalism in the IG predator can also alter the effect of enrichment, preventing predator-mediated extinction of the IG prey at high productivities predicted by simple models. Cannibalism in the IG prey can reverse the effect of top-down cascades, leading to an increase in the resource with decreasing IG predator density. These predictions are consistent with current data. Overall, cannibalism promotes the coexistence of the IG predator and IG prey. These results indicate that including cannibalism in current models can overcome the discrepancy between theory and empirical data. Thus, we need to measure and account for cannibalistic interactions to reliably predict the structure and dynamics of communities.

Background Terminal restriction fragment length polymorphism (T-RFLP) analysis is a common DNA-fingerprinting technique used for comparisons of complex microbial communities. Although the technique is well established there is no consensus on how to treat T-RFLP data to achieve the highest possible accuracy and reproducibility. This study focused on two critical steps in the T-RFLP data treatment: the alignment of the terminal restriction fragments (T-RFs), which enables comparisons of samples, and the normalization of T-RF profiles, which adjusts for differences in signal strength, total fluorescence, between samples. Results Variations in the estimation of T-RF sizes were observed and these variations were found to affect the alignment of the T-RFs. A novel method was developed which improved the alignment by adjusting for systematic shifts in the T-RF size estimations between the T-RF profiles. Differences in total fluorescence were shown to be caused by differences in sample concentration and by the gel loading. Five normalization methods were evaluated and the total fluorescence normalization procedure based on peak height data was found to increase the similarity between replicate profiles the most. A high peak detection threshold, alignment correction, normalization and the use of consensus profiles instead of single profiles increased the similarity of replicate T-RF profiles, i.e. lead to an increased reproducibility. The impact of different treatment methods on the outcome of subsequent analyses of T-RFLP data was evaluated using a dataset from a longitudinal study of the bacterial community in an activated sludge wastewater treatment plant. Whether the alignment was corrected or not and if and how the T-RF profiles were normalized had a substantial impact on ordination analyses, assessments of bacterial dynamics and analyses of correlations with environmental parameters. Conclusions A novel method for the evaluation and correction of the alignment of T-RF profiles was shown to reduce the uncertainty and ambiguity in alignments of T-RF profiles. Large differences in the outcome of assessments of bacterial community structure and dynamics were observed between different alignment and normalization methods. The results of this study can therefore be of value when considering what methods to use in the analysis of T-RFLP data.

The long-term data on structural characteristics of phytoplankton (1954–2014) and zooplankton (2004–2013), as well as chlorophyll content in the water and bottom sediments (2009–2014) in the Rybinsk Reservoir (Upper Volga, Russia) were analyzed. It was shown that the modern climate changes lead to transformation in the state and dynamics of biological communities that is characteristic of the trophicity increase. After the abnormally hot summer of 2010 a sharp rise in chlorophyll content in water with a predominance of values typical for eutrophic and highly eutrophic conditions was detected. Distribution of plant pigments in the bottom sediments was similar in different years, which shows the specific character of the sediment complex structure in the reservoir. In the seasonal dynamics of phytoplankton biomass and chlorophyll concentration the summer maximum caused by development of cyanobacteria began to dominate above the spring one. In the structure of phytoplankton the proportions of cyanobacteria and myxotrophic phytophagellates increased, the invasion of brackish-water diatoms was marked, and diminution of the cell size was noted. In seasonal dynamics of zooplankton biomass the second late peak was formed in August and it was particularly pronounced in the abnormally hot summer of 2010. In addition, there was a 1–2 week shift in timing of the beginning and ending in seasonal cycle of a number of zooplankton species relative to the 1960–1970s. Appearance of a summer dissolved oxygen deficiency (up to 1–4 mg O2/L in the layer of 1–7 m above the bottom) resulted in a local change in the vertical distribution of crustacean filtrators and decrease in their abundance up to three times

This study aimed at describing the phytoplankton dynamics and structure in a shallow eutrophic reservoir, the Garças Pond, located in the Parque Estadual das Fontes do Ipiranga (23°38'40.6'' S, 46°37'28.0'' W), in the Municipality of São Paulo, southeast Brazil. Samples were collected monthly from January to December 1997 in five depths (subsurface, 1 m, 2 m, 3 m, and 20 cm above the bottom) in the pelagic zone (Z max = 4.7 m). Abiotic variables studied were: water temperature, turbidity, transparency, conductivity, pH, dissolved oxygen, alkalinity, inorganic carbon, and N and P dissolved and total forms. Altogether 236 phytoplankton taxa distributed among 10 classes were identified. Phytoplankton seasonal and vertical variation was related to shifts in the water chemical features as a consequence of a warm-wet season with stratified water column (phase 1, January-March and September-December) alternating with a cool-dry season with mixed water column (phase 2, April-August). There were shifts in cyanobacterial dominance over the entire year. During phase 1, Raphidiopsis/Cylindrospermopsis was one of the most important taxon. During phase 2, Raphidiopsis/Cylindrospermopsis biomass decreased, whereas richness and diversity increased and diatoms were relatively abundant. In September, when the water column was markedly stratified, a cyanobacterial bloom (Sphaerocavum brasiliense) occurred. Changes in water chemical variables caused by the bloom allowed recognition of a phase 3, in which pH and chlorophyll a, TP and CO₃ ²⁻ concentration reached their highest values. According to Reynolds and collaborators' functional groups approach, phase 1 was marked by groups S/W1/W2/H1/Y, phase 2 by groups K/L M /L O /D/P/X1/F, and phase 3 by group M. This sequence was corroborated by canonical correspondence analysis (CCA) results.

The synthesis of biodegradable plastic PHA from organic waste through mixed microbial cultures (PHA-MMCs), at extremely low cost, has the potential for expanded production. However, the dynamics of dominant species in PHA-MMCs are poorly understood. Our results demonstrate for the first time the impact of phages on the structure of bacterial communities in the PHA-MMCs. There are complex interactions between the PHA producers (e.g., Azomonas , Paracoccus , and Thauera ) and phages (e.g., Casadabanvirus and unclassified Hendrixvirinae). Phage communities can regulate the activity and structure of bacterial communities. In addition, the AMGs related to PHA synthesis may hitchhike during phage-host infection cycles, enabling their dissemination across bacterial communities, and phages may act as a critical genetic reservoir for bacterial members, facilitating access to PHA synthesis-related functional traits. This study highlights the impact of phages on bacterial community structure, suggesting that phages have the potential to be used as a tool for better controlling the microbial community structure of PHA-MMCs.

Members of the rhizosphere exhibit dynamic patterns of activity and dormancy. This study stresses the need to focus on active microbial communities to detect temporal changes in plant microbiomes. Additionally, the metabolic activity of microbes should be considered a key determinant of core microbiome membership. Parallel patterns in active community dynamics between fungal and bacterial communities provide a potentially generalizable rule of microbial community temporal dynamics in plant rhizospheres.

The diversity and community structure of arbuscular mycorrhizal fungi (AMF) associated with coconut (Cocos nucifera) roots was evaluated by next generation sequencing (NGS) using partial sequences of the 18S rDNA gene and by spore isolation and morphological identification from rhizosphere soil. Root samples from six different Green Dwarf coconut plantations and from one organic plantation surrounded by tropical dry forest along the coastal sand dunes in Yucatan, Mexico, were collected during the rainy and dry seasons. In total, 14 root samples were sequenced with the Illumina MiSeq platform. Additionally, soil samples from the dry season were collected to identify AMF glomerospores. Based on a 95–97% similarity, a total of 36 virtual taxa (VT) belonging to nine genera were identified including one new genus-like clade. Glomus was the most abundant genus, both in number of VT and sequences. The comparison of dry and rainy season samples revealed differences in the richness and composition of AMF communities colonizing coconut roots. Our study shows that the main AMF genera associated with coconut tree roots in all samples were Glomus, Sclerocystis, Rhizophagus, Redeckera, and Diversispora. Based on glomerospore morphology, 22 morphospecies were recorded among which 14 were identified to species. Sclerocystis sinuosa, Sclerocystis rubiformis, Glomus microaggregatum, and Acaulospora scrobiculata were dominant in field rhizosphere samples. This is the first assessment of the composition of AMF communities colonizing coconut roots in rainy and dry seasons. It is of importance for selection of AMF species to investigate for their potential application in sustainable agriculture of coconut.

Benthic cyanobacteria can respond rapidly to favorable environmental conditions, overgrow a variety of reef organisms, and dominate benthic marine communities; however, little is known about the dynamics and consequences of such cyanobacterial blooms in coral reef ecosystems. In this study, the benthic community was quantified at the time of coral spawnings in Guam to assess the substrate that coral larvae would encounter when attempting settlement. Transects at 9, 18, and 25-m depths were surveyed at two reef sites before and after heavy wave action driven by westerly monsoon winds. Communities differed significantly between sites and depths, but major changes in benthic community structure were associated with wave action driven by monsoon winds. A shift from cyanobacteria to crustose coralline algae (CCA) accounted for 44% of this change. Coral recruitment on Guam may be limited by substrate availability if cyanobacteria cover large areas of the reef at the time of settlement, and consequently recruitment may in part depend upon wave action from annual monsoon winds and tropical storms which remove cyanobacteria, thereby exposing underlying CCA and other substrate suitable for coral settlement.

This study aimed at analyzing the environmental factors which determine the structure and dynamic of phytoplankton in a shallow reservoir with abundant macrophyte flora, Ninféias Pond (Brazil). It is hypothesized that, although its shallowness, periodic stratifications play an important role on its phytoplankton community. Water samples were collected monthly, from January to December 1997, in four depths (sub-surface, 1 m, 2 m, and bottom) of pelagic zone ( Z max  = 3.6 m). Community seasonal and vertical variations followed a hot-rainy season with water column stratification (phase 1; Q index: medium ), alternating with a cool-dry season with water column mixing (phase 2: Q index: excellent ). Nanoplanktonic flagellates dominated, mainly mixotrophic species. During phase 1, Chlamydomonas sp. ( G ) was the main species, dominating at the anoxic and nutrient-rich hypolimnion. At the same time, richness and diversity were relatively lower. During phase 2, lower water temperatures and higher dissolved oxygen concentrations favoured the prymnesiophyte Chrysochromulina cf. breviturrita ( X2 ). Sequence of functional groups over phases 1 and 2 was: phase 1 =  G  → transition =  Y/P/E/D/F/W2/X3  → phase 2 =  X2/Lo/X1 ; most of these groups have been associated to oligo-mesotrophic systems. Seasonal stratifications played a decisive role in determining the structure and dynamic of phytoplankton in the Ninféias Pond. However, in such a complex and heterogeneous system, other compartments of the food web (macrophytes, zooplankton, fishes) may also act as relevant driving forces, in synergy with the physical and chemical environment.

This chapter contains sections titled: Population ecology and community ecology theory People Research activities and questions Methods of study Feral pigs as a model system for studying applied ecology Structure of the book