Vertical Stratification of Insect Species Developing in Water-Filled Tree Holes

Forest ecosystems have a distinct vertical dimension, but the structuring of communities in this three-dimensional space is not well understood. Water-filled tree holes are natural microcosms structured in metacommunities. Here, we used these microcosms as model systems to analyze how insect communities and the occurrence and abundance of individual species are influenced by biotic and abiotic microhabitat characteristics, the vertical position of the tree hole, and stand-scale habitat availability. We found that both the characteristics of water-filled tree holes and their insect communities differ significantly between canopy and ground level. Individual insect species showed contrasting responses to the vertical position of the tree holes when important environmental factors at the stand and the tree-hole scale were considered. While some species, such as the mosquito Aedes geniculatus and the beetle Prionocyphon serricornis, decreased in abundance with increasing tree-hole height, the biting midge Dasyhelea sp., the non-biting midge Metriocnemus cavicola and the hoverfly Myiatropa florea increased in abundance. Our results suggest that vertical stratification in forests is most likely driven not only by variation in tree-hole microhabitat properties, i.e., niche separation, but also by individual species traits, such as adult dispersal propensity, food preferences and mating behavior of adult stages, and interspecific competition of larval stages. Therefore, communities of insect species developing in tree holes are likely structured by competition–colonization trade-offs predicted by metacommunity theory.

In situ visualization of glycoside hydrolase family 92 genes in marine flavobacteria

Gene clusters rich in carbohydrate-active enzymes within Flavobacteriia genera provide a competitiveness for their hosts to degrade diatom-derived polysaccharides. One such widely distributed polysaccharide is glucuronomannan, a main cell wall component of diatoms. A conserved gene cluster putatively degrading glucuronomannan was found previously among various flavobacterial taxa in marine metagenomes. Here, we aimed to visualize two glycoside hydrolase family 92 genes coding for α-mannosidases with fluorescently-labeled polynucleotide probes using direct-geneFISH. Reliable in situ localization of single-copy genes was achieved with an efficiency up to 74% not only in the flavobacterial strains Polaribacter Hel1_33_49 and Formosa Hel1_33_131 but also in planktonic samples from the North Sea. In combination with high-resolution microscopy, direct-geneFISH gave visual evidence of the contrasting lifestyles of closely related Polaribacter species in those samples and allowed for the determination of gene distribution among attached and free-living cells. We also detected highly similar GH92 genes in yet unidentified taxa by broadening probe specificities, enabling a visualization of the functional trait in subpopulations across the borders of species and genera. Such a quantitative insight into the niche separation of flavobacterial taxa complements our understanding of the ecology of polysaccharide-degrading bacteria beyond omics-based techniques on a single-cell level.

Factors Promoting Coexistence between Endemic Ants and Invasive Wasps

<p>Invasive animals can alter the community composition of native ecosystems by means of competition and predation. In this study I investigated the factors that may facilitate coexistence between endemic ants and invasive wasps. Previous research has shown that entire communities can be impacted by invasions. Endemic species subject to pressure from invasive species may undergo a niche shift to enable coexistence and minimise the impact of this pressure. The invertebrate community composition of Nothofagus forests in the South Island of New Zealand has been altered by predation from Invasive Vespula wasps. Ants and wasps in this ecosystem coexist on the same trophic level; they simultaneously fill multiple trophic roles as primary predators, secondary predators, and primary consumers. The outcome of competition between species such as ants and wasps is not easy to predict, and may vary in different communities and with different densities of competitors. In this dissertation I aimed to determine the extent to which competition occurs between native ants and invasive Vespula wasps, and to investigate the impacts of invasion on the native invertebrate community. I quantified the invertebrate community composition of Nothofagus forests and then experimentally reduced wasp numbers to investigate any changes as a result of a reduction in predation or competition. The observed changes in community composition were as a result of differing abundances of taxonomic groups within my study sites. In order to more robustly determine the community effects of wasp removal it may be necessary to reduce wasp numbers by up to 90% for many years. Even under these conditions, species that are particularly vulnerable to wasp predation or competition may have already been permanently excluded from this system. I then investigated temporal niche shifts by native ants when faced with reduced competition for food resources from invasive wasps. There was an increase in the numbers of ants foraging on honeydew when I experimentally reduced wasp numbers. This increase may be due to increases in both the quantity and quality of the available honeydew. When densities of wasps were substantially reduced there was a difference in the foraging abundances of ants and wasps; however, there was no change in the overall temporal foraging pattern of ants. Isotope ratios and consequently trophic levels of native competitors may change in response to the removal of an invasive species. To test this I examined changes in isotope ratios as a result of removal of wasps. The observed changes in the trophic levels of both ants and wasps appear to be a result of natural seasonal variation in consumption related to the nutritional requirements of the colony. Finally, I examined behavioral interactions between native ants and invasive wasps during foraging. This study has indicated that wasps may find and access resources more readily when ants are present. Native ants may facilitate foraging by wasps, as demonstrated by the increase in wasp numbers when foraging in the presence of ants. Additionally, the impact of competition between wasps and ants is likely to be density dependant. Co-occurrence between endemic and invasive competitors is possible through two important mechanisms, niche separation and behavioural adaptations. Native ants in this system are able to forage in different temporal niches than invasive wasps, and their dominant behaviour serves to diminish competitive interactions. These findings have implications for the ecology of these forests in understanding the considerable impact that invasive species may have on native ecosystems and particularly those species which have similar resource requirements.</p>

Factors Promoting Coexistence between Endemic Ants and Invasive Wasps

<p>Invasive animals can alter the community composition of native ecosystems by means of competition and predation. In this study I investigated the factors that may facilitate coexistence between endemic ants and invasive wasps. Previous research has shown that entire communities can be impacted by invasions. Endemic species subject to pressure from invasive species may undergo a niche shift to enable coexistence and minimise the impact of this pressure. The invertebrate community composition of Nothofagus forests in the South Island of New Zealand has been altered by predation from Invasive Vespula wasps. Ants and wasps in this ecosystem coexist on the same trophic level; they simultaneously fill multiple trophic roles as primary predators, secondary predators, and primary consumers. The outcome of competition between species such as ants and wasps is not easy to predict, and may vary in different communities and with different densities of competitors. In this dissertation I aimed to determine the extent to which competition occurs between native ants and invasive Vespula wasps, and to investigate the impacts of invasion on the native invertebrate community. I quantified the invertebrate community composition of Nothofagus forests and then experimentally reduced wasp numbers to investigate any changes as a result of a reduction in predation or competition. The observed changes in community composition were as a result of differing abundances of taxonomic groups within my study sites. In order to more robustly determine the community effects of wasp removal it may be necessary to reduce wasp numbers by up to 90% for many years. Even under these conditions, species that are particularly vulnerable to wasp predation or competition may have already been permanently excluded from this system. I then investigated temporal niche shifts by native ants when faced with reduced competition for food resources from invasive wasps. There was an increase in the numbers of ants foraging on honeydew when I experimentally reduced wasp numbers. This increase may be due to increases in both the quantity and quality of the available honeydew. When densities of wasps were substantially reduced there was a difference in the foraging abundances of ants and wasps; however, there was no change in the overall temporal foraging pattern of ants. Isotope ratios and consequently trophic levels of native competitors may change in response to the removal of an invasive species. To test this I examined changes in isotope ratios as a result of removal of wasps. The observed changes in the trophic levels of both ants and wasps appear to be a result of natural seasonal variation in consumption related to the nutritional requirements of the colony. Finally, I examined behavioral interactions between native ants and invasive wasps during foraging. This study has indicated that wasps may find and access resources more readily when ants are present. Native ants may facilitate foraging by wasps, as demonstrated by the increase in wasp numbers when foraging in the presence of ants. Additionally, the impact of competition between wasps and ants is likely to be density dependant. Co-occurrence between endemic and invasive competitors is possible through two important mechanisms, niche separation and behavioural adaptations. Native ants in this system are able to forage in different temporal niches than invasive wasps, and their dominant behaviour serves to diminish competitive interactions. These findings have implications for the ecology of these forests in understanding the considerable impact that invasive species may have on native ecosystems and particularly those species which have similar resource requirements.</p>

Niche separation in cross-feeding sustains bacterial strain diversity across nutrient environments and may increase chances for survival in nutrient-limited leaf apoplasts

The leaf microbiome plays a crucial role in plant's health and resilience to stress. Like in other hosts, successful colonization is dependent on multiple factors, among them, resource accessibility. The apoplast is an important site of plant-microbe interactions where nutrients are tightly regulated. While leaf pathogens have evolved elaborate strategies to obtain nutrients there, it is not yet clear how commensals survive without most of these adaptations. Resource limitation can promote metabolic interactions, which in turn shape and stabilize microbiomes but this has not been addressed in detail in leaves. Here, we investigated whether and how the nutrient environment might influence metabolic exchange and assembly of bacterial communities in Flaveria trinervia and F. robusta leaves. We enriched bacteria from both plant species in-vitro in minimal media with sucrose as a carbon source, and with or without amino acids. After enrichment, we studied the genetic and metabolic diversity within the communities. Enriched Pseudomonas koreensis strains could cross-feed from diverse leaf bacteria. Although P. koreensis could not utilize sucrose, cross-feeding diverse metabolites from Pantoea sp ensured their survival in the sucrose-only enrichments. The Pseudomonas strains had high genetic similarity (~99.8% ANI) but still displayed clear niche partitioning, enabling them to simultaneously cross-feed from Pantoea. Interestingly, cross-feeders were only enriched from F. robusta and not from F. trinervia. Untargeted metabolomics analysis of the leaf apoplasts revealed contrasting nutrient environments, with greater concentrations of high-cost amino acids in F. trinervia. Additionally, P. koreensis strains were better able to survive without a cross-feeding partner in these richer apoplasts. Thus, cross feeding might arise as an adaptation to cope with nutrient limitations in the apoplast. Understanding how apoplast resources influence metabolic interactions could therefore provide plant breeders targets to manipulate leaf microbiome shape and stability.

Niche Differentiation of Arsenic-Transforming Microbial Groups in the Rice Rhizosphere Compartments as Impacted by Water Management and Soil-Arsenic Concentrations

Arsenic (As) bioavailability in the rice rhizosphere is influenced by many microbial interactions, particularly by metal-transforming functional groups at the root-soil interface. This study was conducted to examine As-transforming microbes and As-speciation in the rice rhizosphere compartments, in response to two different water management practices (continuous and intermittently flooded), established on fields with high to low soil-As concentration. Microbial functional gene composition in the rhizosphere and root-plaque compartments were characterized using the GeoChip 4.0 microarray. Arsenic speciation and concentrations were analyzed in the rhizosphere soil, root-plaque, pore water, and grain samples. Results confirmed several As-biotransformation processes in the rice rhizosphere compartments, and distinct assemblage of As-reducing and methylating bacteria was observed between the root-plaque and rhizosphere. Results confirmed higher potential for microbial As-reduction and As-methylation in continuously flooded, long term As-contaminated fields, which accumulated highest concentrations of AsIII and methyl-As concentrations in pore water and rice grains. Water management treatment significantly altered As-speciation in the rhizosphere, and intermittent flooding reduced methyl-As and AsIII concentrations in the pore water, root-plaque and rice grain. Ordination and taxonomic analysis of detected gene-probes indicated that root-plaque and rhizosphere assembled significantly different microbial functional groups demonstrating niche separation. Taxonomic non-redundancy was evident, suggesting that As-reduction, -oxidation and -methylation processes were performed by different microbial functional groups. It was also evident that As transformation was coupled to different biogeochemical cycling processes (nutrient assimilation, carbon metabolism etc.) in the compartments and between treatments, revealing functional non-redundancy of rice-rhizosphere microbiome in response to local biogeochemical conditions and As contamination. This study provided novel insights on As-biotransformation processes and their implications on As-chemistry at the root-soil interface and their responses to water management, which could be applied for mitigating As-bioavailability and accumulation in rice grains.

Comammox Nitrospira bacteria outnumber canonical nitrifiers irrespective of electron donor mode and availability

Complete ammonia oxidizing bacteria coexist with canonical ammonia and nitrite oxidizing bacteria in a wide range of environments. Whether this coexistence is due to competitive or cooperative interactions between the three guilds, or a result of niche separation is not yet clear. Understanding the factors driving coexistence of nitrifying guilds is critical to effectively manage nitrification processes occurring in engineered and natural ecosystems. In this study, microcosms-based experiments were used to investigate the impact of electron donor mode (i.e., ammonia and urea) and loading on the population dynamics of nitrifying guilds in drinking water biofilter media. Shotgun sequencing of DNA from select time points followed by co-assembly and re-construction of metagenome assembled genomes (MAGs) revealed multiple clade A2 and one clade A1 comammox bacterial populations coexisted in the microcosms alongside Nitrosomonas-like ammonia oxidizers and Nitrospira-like nitrite oxidizer populations. Clade A2 comammox bacteria were likely the primary nitrifiers within the microcosms and increased in abundance over canonical ammonia and nitrite oxidizing bacteria irrespective of electron donor mode or nitrogen loading rates. This suggests that comammox bacteria will outnumber nitrifying communities sourced from oligotrophic environments irrespective of variable nitrogen regimes. Changes in comammox bacterial abundance were not correlated with either ammonia or nitrite oxidizing bacterial abundance in urea amended systems where metabolic reconstruction indicated potential cross feeding between ammonia and nitrite oxidizing bacteria. In contrast, comammox bacterial abundance demonstrated a negative correlation with that of nitrite oxidizers in ammonia amended systems. This suggests that potentially weaker synergistic relationships between ammonia and nitrite oxidizers might enable comammox bacteria to displace nitrite oxidizers from complex nitrifying communities.

Relevance of Candidatus Nitrotoga for nitrite oxidation in technical nitrogen removal systems

Many biotechnological applications deal with nitrification, one of the main steps of the global nitrogen cycle. The biological oxidation of ammonia to nitrite and further to nitrate is critical to avoid environmental damage and its functioning has to be retained even under adverse conditions. Bacteria performing the second reaction, oxidation of nitrite to nitrate, are fastidious microorganisms that are highly sensitive against disturbances. One important finding with relevance for nitrogen removal systems was the discovery of the mainly cold-adapted Cand. Nitrotoga, whose activity seems to be essential for the recovery of nitrite oxidation in wastewater treatment plants at low temperatures, e.g., during cold seasons. Several new strains of this genus have been recently described and ecophysiologically characterized including genome analyses. With increasing diversity, also mesophilic Cand. Nitrotoga representatives have been detected in activated sludge. This review summarizes the natural distribution and driving forces defining niche separation in artificial nitrification systems. Further critical aspects for the competition with Nitrospira and Nitrobacter are discussed. Knowledge about the physiological capacities and limits of Cand. Nitrotoga can help to define physico-chemical parameters for example in reactor systems that need to be run at low temperatures. Key points • Characterization of the psychrotolerant nitrite oxidizer Cand. Nitrotoga • Comparison of the physiological features of Cand. Nitrotoga with those of other NOB • Identification of beneficial environmental/operational parameters for proliferation