Katja Meuser

Classifying the bacterial gut microbiota of termites and cockroaches: A curated phylogenetic reference database (DictDb)

Recent developments in sequencing technology have given rise to a large number of studies that assess bacterial diversity and community structure in termite and cockroach guts based on large amplicon libraries of 16S rRNA genes. Although these studies have revealed important ecological and evolutionary patterns in the gut microbiota, classification of the short sequence reads is limited by the taxonomic depth and resolution of the reference databases used in the respective studies. Here, we present a curated reference database for accurate taxonomic analysis of the bacterial gut microbiota of dictyopteran insects. The Dictyopteran gut microbiota reference Database (DictDb) is based on the Silva database but was significantly expanded by the addition of clones from 11 mostly unexplored termite and cockroach groups, which increased the inventory of bacterial sequences from dictyopteran guts by 26%. The taxonomic depth and resolution of DictDb was significantly improved by a general revision of the taxonomic guide tree for all important lineages, including a detailed phylogenetic analysis of the Treponema and Alistipes complexes, the Fibrobacteres, and the TG3 phylum. The performance of this first documented version of DictDb (v. 3.0) using the revised taxonomic guide tree in the classification of short-read libraries obtained from termites and cockroaches was highly superior to that of the current Silva and RDP databases. DictDb uses an informative nomenclature that is consistent with the literature also for clades of uncultured bacteria and provides an invaluable tool for anyone exploring the gut community structure of termites and cockroaches.

The bacterial microbiota in the ceca of Capercaillie (Tetrao urogallus) differs between wild and captive birds

The diet of wild capercaillie differs strongly between seasons. Particularly during winter, when energy demands are high and the birds forage solely on coniferous needles, microbial fermentations in the ceca are considered to contribute significantly to the energy requirement and to the detoxification of the resinous diet. Here, we present the first cultivation-independent analysis of the bacterial community in the cecum of capercaillie, using the 16S rRNA gene as a molecular marker. Cloning and fingerprinting analyses of cecum feces show distinct differences between wild and captive birds. While certain lineages of Clostridiales, Synergistetes, and Actinobacteria are most prevalent in wild birds, they are strongly reduced in individuals raised in captivity. Most striking is the complete absence of Megasphaera and Synergistes species in captive capercaillie, which are characterized by a large abundance of Gammaproteobacteria closely related to members of the genus Anaerobiospirillum, bacteria that are commonly connected with intestinal dysfunction. The community profiles of cecum content from wild birds differed between summer and winter season, and the cecum wall may be an important site for bacterial colonization. Our results corroborate the hypothesis that the bacterial community in the ceca of tetraonid birds changes in response to their highly specialized seasonal diets. Moreover, we propose that the observed differences in community profiles between wild and captive capercaillie reflects a disturbance in the bacterial microbiota that compromises the performance of the cecum and may be responsible for the high mortality of captive birds released into nature.

Population Structure of Endomicrobia in Single Host Cells of Termite Gut Flagellates (Trichonympha spp.)

The gut microbiota of many phylogenetically lower termites is dominated by the cellulolytic flagellates of the genus Trichonympha, which are consistently associated with bacterial symbionts. In the case of Endomicrobia, an unusual lineage of endosymbionts of the Elusimicrobia phylum that is also present in other gut flagellates, previous studies have documented strict host specificity, leading to the cospeciation of “Candidatus Endomicrobium trichonymphae” with their respective flagellate hosts. However, it currently remains unclear whether one Trichonympha species is capable of harboring more than one Endomicrobia phylotype. In the present study, we selected single Trichonympha cells from the guts of Zootermopsis nevadensis and Reticulitermes santonensis and characterized their Endomicrobia populations based on internal transcribed spacer (ITS) region sequences. We found that each host cell harbored a homogeneous population of symbionts that were specific to their respective host species, but phylogenetically distinct between each host lineage, corroborating cospeciation being caused by vertical inheritance. The experimental design of the present study also allowed for the identification of an unexpectedly large amount of tag-switching between samples, which indicated that any high-resolution analysis of microbial community structures using the pyrosequencing technique has to be interpreted with great caution.

Comparison of two different methods to measure nitric oxide turnover in soils

Abstract The NO turnover in soils was measured in two different experimental set-ups, a flow-through system, which is very time-consuming and needs rather sophisticated equipment, and a closed system using serum bottles. We compared the NO turnover parameters (NO consumption rate constant, NO production rate, NO compensation concentration) that were measured with both systems in different soils, under different conditions and in the presence of 10 Pa acetylene to inhibit nitrification. The values of the NO turnover parameters that were measured with the two systems under oxic conditions were usually comparable. The addition of acetylene did not affect the NO consumption rate constants of the soils with the exception of soil G1. However, the NO production rates and the NO compensation concentrations decreased significantly in the presence of acetylene, indicating that nitrification was the main source of NO in these soils. Only one soil (Bol) showed no nitrifying activity. Increasing soil moisture content resulted in decreasing NO consumption rate constants and NO production rates. Even at a high soil moisture content of 80% water holding capacity, nitrification was the main source of NO. The values of the NO turnover parameters that were measured with the two systems were not comparable under anoxic conditions. The NO consumption rate constants and the NO production rates were much lower in the closed than in the flow-through system, indicating that the NO consumption activity became saturated by the high NO concentrations accumulating in the closed system. Under oxic conditions, however, closed serum bottles were a cheap, easy and reliable tool with which to determine NO turnover parameters and to distinguish between nitrification and denitrification as sources of NO.

Hydrogen consumption and carbon monoxide production in soils with different properties

Abstract Soils are the dominant sink in the global budget of atmospheric H2, and can be an important local source of atmospheric CO. In order to understand which soil characteristics affect the rates of H2 consumption and CO production, we measured these activities in 16 different soils at 30% and 60% of their maximum water holding capacity (whc). The soils were obtained from forests, meadows and agricultural fields in Germany and exhibited different characteristics with respect to texture, pH, total C, substrate-induced respiration (SIR), respiration, total and inorganic N, N mineralization, nitrification, N2O production and NO turnover. The H2 consumption rate constants were generally lower at 60% than at 30% whc, whereas the CO production rates were not influenced by the whc. Spearman correlation analysis showed that H2 consumption correlated significantly (r>0.5, P<0.05) at both water contents only with SIR and potential nitrification. The correlation with these variables that are largely dominated by soil microorganisms is consistent with our understanding that atmospheric H2 is oxidized by soil hydrogenases. Multiple regression analysis and factor analysis gave similar results. Production of CO, on the other hand, was significantly correlated to soil total C, respiration, total N and NH4+. The correlation with these variables that are largely dominated by a soils chemical composition is consistent with our understanding that CO is produced by chemical oxidation of soil organic C. CO production was also influenced by soil usage, with rates increasing in the order: arable

Microenvironmental heterogeneity of gut compartments drives bacterial community structure in wood- and humus-feeding higher termites.

ABSTRACT Symbiotic digestion of lignocellulose in higher termites (family Termitidae) is accomplished by an exclusively prokaryotic gut microbiota. By deep sequencing of amplified 16S rRNA genes, we had identified diet as the primary determinant of bacterial community structure in a broad selection of termites specialized on lignocellulose in different stages of humification. Here, we increased the resolution of our approach to account for the pronounced heterogeneity in microenvironmental conditions and microbial activities in the major hindgut compartments. The community structure of consecutive gut compartments in each species strongly differed, but that of homologous compartments clearly converged, even among unrelated termites. While the alkaline P1 compartments of all termites investigated contained specific lineages of Clostridiales, the posterior hindgut compartments (P3, P4) differed between feeding groups and were predominantly colonized by putatively fiber‐associated lineages of Spirochaetes, Fibrobacteres and the TG3 phylum (wood and grass feeders) or diverse assemblages of Clostridiales and Bacteroidetes (humus and soil feeders). The results underscore that bacterial community structure in termite guts is driven by microenvironmental factors, such as pH, available substrates and gradients of O2 and H2, and inspire investigations on the functional roles of specific bacterial taxa in lignocellulose and humus digestion. &NA; Graphical Abstract Figure. Microenvironmental differences shape the distribution and abundance of bacterial populations in the gut compartments of higher termites.

Exclusive Gut Flagellates of Serritermitidae Suggest a Major Transfaunation Event in Lower Termites: Description of Heliconympha glossotermitis gen. nov. spec. nov.

The guts of lower termites are inhabited by host‐specific consortia of cellulose‐digesting flagellate protists. In this first investigation of the symbionts of the family Serritermitidae, we found that Glossotermes oculatus and Serritermes serrifer each harbor similar parabasalid morphotypes: large Pseudotrichonympha‐like cells, medium‐sized Leptospironympha‐like cells with spiraled bands of flagella, and small Hexamastix‐like cells; oxymonadid flagellates were absent. Despite their morphological resemblance to Pseudotrichonympha and Leptospironympha, a SSU rRNA‐based phylogenetic analysis identified the two larger, trichonymphid flagellates as deep‐branching sister groups of Teranymphidae, with Leptospironympha sp. (the only spirotrichosomid with sequence data) in a moderately supported basal position. Only the Hexamastix‐like flagellates are closely related to trichomonadid flagellates from Rhinotermitidae. The presence of two deep‐branching lineages of trichonymphid flagellates in Serritermitidae and the absence of all taxa characteristic of the ancestral rhinotermitids underscores that the flagellate assemblages in the hindguts of lower termites were shaped not only by a progressive loss of flagellates during vertical inheritance but also by occasional transfaunation events, where flagellates were transferred horizontally between members of different termite families. In addition to the molecular phylogenetic analyses, we present a detailed morphological characterization of the new spirotrichosomid genus Heliconympha using light and electron microscopy.

High-resolution phylogenetic analysis of Endomicrobia reveals multiple acquisitions of endosymbiotic lineages by termite gut flagellates

Bacteria of the class Endomicrobia form a deep-branching clade in the Elusimicrobia phylum. They are found almost exclusively in the intestinal tract of animals and are particularly abundant in many termites, where they reside as intracellular symbionts in the cellulolytic gut flagellates. Although small populations of putatively free-living lineages have been detected in faunated and flagellate-free hosts, the evolutionary origin of the endosymbionts is obscured by the limited amount of phylogenetic information provided by the 16S rRNA gene fragment amplified with Endomicrobia-specific primers. Here, we present a robust phylogenetic framework based on the near-full-length 16S-23S rRNA gene region of a diverse set of Endomicrobia from termites and cockroaches, which also allowed us to classify the shorter reads from previous studies. Our data revealed that endosymbionts arose independently at least four times from different free-living lineages, which were already present in ancestral cockroaches but became associated with their respective hosts long after the digestive symbiosis between termites and flagellates had been established. Pyrotag sequencing revealed that the proportion of putatively free-living lineages increased, when all flagellates and their symbionts were removed from the gut of lower termites by starvation, starch feeding or hyperbaric oxygen, but results varied between different methods.

Phylogeny and Ultrastructure of Oxymonas jouteli, a Rostellum-free Species, and Opisthomitus longiflagellatus sp. nov., Oxymonadid Flagellates from the Gut of Neotermes jouteli

The biodiversity of oxymonadid flagellates in termite hindguts is not fully explored. Many species have been differentiated only by morphological features, and small-celled species have been overlooked or ignored. Our analysis of the dry wood termite Neotermes jouteli by light and electron microscopy revealed the presence of two distinct morphotypes of oxymonads. The larger one matched the morphology of Oxymonas jouteli, the only oxymonad species described from this termite. Although it generally lacks the typical anterior rostellum of the genus Oxymonas, its SSU rRNA gene sequence clusters among other members of this genus, including novel phylotypes that we obtained from Incisitermes tabogae. The second morphotype was a tiny oxymonad that showed the typical traits of the genus Opisthomitus, including a pointed anterior prolongation (lappet). However, the four equal flagella were much longer than those of Opisthomitus avicularis from Kalotermes flavicollis, the only species of the genus and so far described only by light microscopy. We provide a detailed description of Opisthomitus longiflagellatus sp. nov. and demonstrate that despite ultrastructural similarities to members of the Polymastigidae, its SSU rRNA gene sequences form a separate family-level lineage with a slight affinity to the Pyrsonymphidae.