Microplastic ingestion affects hydrogen production and microbiomes in the gut of the terrestrial isopod Porcellio scaber

Microplastic (MP) is an environmental burden and enters food webs via ingestion by macrofauna, including isopods (Porcellio scaber) in terrestrial ecosystems. Isopods represent ubiquitously abundant, ecologically important detritivores. However, MP-polymer specific effects on the host and its gut microbiota are unknown. We tested the hypothesis that biodegradable (polylactic acid [PLA]) and non-biodegradable (polyethylene terephthalate [PET]; polystyrene [PS]) MPs have contrasting effects on P. scaber mediated by changes of the gut microbiota. The isopod fitness after an 8-week MP-exposure was generally unaffected, although the isopods showed avoidance behaviour to PS-food. MP-polymer specific effects on gut microbes were detected, including a stimulation of microbial activity by PLA compared with MP-free controls. PLA stimulated hydrogen emission from isopod guts, while PET and PS were inhibitory. We roughly estimated 107 kg year−1 hydrogen emitted from the isopods globally and identified their guts as anoxic, significant mobile sources of reductant for soil microbes despite the absence of classical obligate anaerobes, likely due to Enterobacteriaceae-related fermentation activities that were stimulated by lactate generated during PLA-degradation. The findings suggest negative effects of PET and PS on gut fermentation, modulation of important isopod hydrogen emissions by MP pollution and the potential of MP to affect terrestrial food webs

Effects of microplastic ingestion on hydrogen production and microbiomes in the gut of the terrestrial isopod Porcellio scaber

Microplastic (MP) pollution is an environmental burden. MP enters food webs via ingestion by macrofauna, including isopods (Porcellio scaber) in terrestrial ecosystems. However, MP-effects on the host and its gut microbiome are largely unknown. We tested the hypothesis that biodegradable (polylactic acid, PLA) and non-biodegradable (polyethylene terephthalate, PET polystyrene, PS) MP have contrasting effects on P. scaber mediated by changes of the associated gut microbiome. Although the isopods avoided food containing PS, isopod fitness after eight-week MP-exposure was unaffected. Qualitative and quantitative 16S rRNA gene and 16S rRNA analyses of gut microbiomes indicated general MP effects, MP-type specific indicator taxa, and stimulation by PLA compared to MP-free controls. Isopods emitted hydrogen, and its production increased and decreased after PLA-food and PET- or PS-food ingestion, respectively, relative to controls as indicated by microsensor measurements. Gut pH was unaffected by MP. We identified the gut of P. scaber as significant mobile source of reductant for soil microbiomes likely due to Enterobacteriaceae related fermentation activities that were stimulated by lactate generated during PLA-degradation. The findings suggest negative effects of PET and PS on gut fermentation, modulation of isopod hydrogen emissions by MP pollution, and the potential of MP to affect terrestrial food webs

Microplastic polymer properties as deterministic factors driving terrestrial plastisphere microbiome assembly and succession in the field

Environmental microplastic (MP) is ubiquitous in aquatic and terrestrial ecosystems providing artificial habitats for microbes. Mechanisms of MP colonization, MP polymer impacts, and effects on soil microbiomes are largely unknown in terrestrial systems. Therefore, we experimentally tested the hypothesis that MP polymer type is an important deterministic factor affecting MP community assembly by incubating common MP polymer types in situ in landfill soil for 14 months. 16S rRNA gene amplicon sequencing indicated that MP polymers have specific impacts on plastisphere microbiomes, which are subsets of the soil microbiome. Chloroflexota, Gammaproteobacteria, certain Nitrososphaerota, and Nanoarchaeota explained differences among MP polymers and time points. Plastisphere microbial community composition derived from different MP diverged over time and was enriched in potential pathogens. PICRUSt predictions of pathway abundances and quantitative PCR of functional marker genes indicated that MP polymers exerted an ambivalent effect on genetic potentials of biogeochemical cycles. Overall, the data indicate that (i) polymer type as deterministic factor rather than stochastic factors drives plastisphere community assembly, (ii) MP impacts greenhouse gas metabolism, xenobiotic degradation and pathogen distribution, and (iii) MP serves as an ideal model system for studying fundamental questions in microbial ecology such as community assembly mechanisms in terrestrial environments

Weathering of calcareous bedrocks is strongly affected by the activity of soil microorganisms

Phosphorus (P) availability in calcareous forest soils is commonly low compared to siliceous soils. The main reason for this is that phosphate ions tend to precipitate with calcium (Ca). Weathering of calcareous rocks and the potential of microorganisms to dissolve calcareous parent material is not fully understood. Therefore, we examined microbial carbonate dissolution and the abundance of phosphorus-solubilizing bacteria in temperate forest soils with contrasting calcareous parent materials. We incubated soil extracts with weathered parent materials (i.e., dolomite and limestone) from two calcareous forest soils differing in P content and determined the rates of P and Ca solubilization. In addition, we determined the abundance of phosphorus-solubilizing bacteria (PSB). We found that the net Ca solubilization rate ranged from 8.8 to 511.1 nmol m(-2) d(-1) across both soils and depths. Calcium dissolution rates were negatively related to pH and positively related to the concentration of organic acids. The gross P solubilization rates were on average 63.6% higher from dolomite (P-poor soil) than from limestone (P-rich soil). The abundance of soil PSB ranged from 3.8 % at the limestone site (P-rich soil) to 24.4 % at the dolomite site (P-poor soil). The higher abundance of PSB in the soil derived from dolomite is in line with the high Ca and P solubilization rates at this site, indicating that PSB abundance is related to rock weathering rates from calcareous soils. Pseudomonadales and Enterobacteriales were by far the two most abundant bacterial orders in the PSB community of both soils and soil depths. In conclusion, this study shows, first, that weathering of calcareous bedrocks is strongly affected by the activity of soil microorganisms, and second, that there is likely a selective pressure in P-poor soils towards a higher abundance of PSB

A Transcriptome—Targeting EcoChip for Assessing Functional Mycodiversity

A functional biodiversity microarray (EcoChip) prototype has been developed to facilitate the analysis of fungal communities in environmental samples with broad functional and phylogenetic coverage and to enable the incorporation of nucleic acid sequence data as they become available from large-scale (next generation) sequencing projects. A dual probe set (DPS) was designed to detect a) functional enzyme transcripts at conserved protein sites and b) phylogenetic barcoding transcripts at ITS regions present in precursor rRNA. Deviating from the concept of GeoChip-type microarrays, the presented EcoChip microarray phylogenetic information was obtained using a dedicated set of barcoding microarray probes, whereas functional gene expression was analyzed by conserved domain-specific probes. By unlinking these two target groups, the shortage of broad sequence information of functional enzyme-coding genes in environmental communities became less important. The novel EcoChip microarray could be successfully applied to identify specific degradation activities in environmental samples at considerably high phylogenetic resolution. Reproducible and unbiased microarray signals could be obtained with chemically labeled total RNA preparations, thus avoiding the use of enzymatic labeling steps. ITS precursor rRNA was detected for the first time in a microarray experiment, which confirms the applicability of the EcoChip concept to selectively quantify the transcriptionally active part of fungal communities at high phylogenetic resolution. In addition, the chosen microarray platform facilitates the conducting of experiments with high sample throughput in almost any molecular biology laboratory

The Complete Set of Genes Encoding Major Intrinsic Proteins in Arabidopsis Provides a Framework for a New Nomenclature for Major Intrinsic Proteins in Plants

Major intrinsic proteins (MIPs) facilitate the passive transport of small polar molecules across membranes. MIPs constitute a very old family of proteins and different forms have been found in all kinds of living organisms, including bacteria, fungi, animals, and plants. In the genomic sequence of Arabidopsis, we have identified 35 different MIP-encoding genes. Based on sequence similarity, these 35 proteins are divided into four different subfamilies: plasma membrane intrinsic proteins, tonoplast intrinsic proteins, NOD26-like intrinsic proteins also called NOD26-like MIPs, and the recently discovered small basic intrinsic proteins. In Arabidopsis, there are 13 plasma membrane intrinsic proteins, 10 tonoplast intrinsic proteins, nine NOD26-like intrinsic proteins, and three small basic intrinsic proteins. The gene structure in general is conserved within each subfamily, although there is a tendency to lose introns. Based on phylogenetic comparisons of maize (Zea mays) and Arabidopsis MIPs (AtMIPs), it is argued that the general intron patterns in the subfamilies were formed before the split of monocotyledons and dicotyledons. Although the gene structure is unique for each subfamily, there is a common pattern in how transmembrane helices are encoded on the exons in three of the subfamilies. The nomenclature for plant MIPs varies widely between different species but also between subfamilies in the same species. Based on the phylogeny of all AtMIPs, a new and more consistent nomenclature is proposed. The complete set of AtMIPs, together with the new nomenclature, will facilitate the isolation, classification, and labeling of plant MIPs from other species

Keeping the shoot above water - submergence triggers antithetical growth responses in stems and petioles of watercress (Nasturtium officinale)

The molecular mechanisms controlling underwater elongation are based extensively on studies on internode elongation in the monocot rice (Oryza sativa) and petiole elongation in Rumex rosette species. Here, we characterize underwater growth in the dicot Nasturtium officinale (watercress), a wild species of the Brassicaceae family, in which submergence enhances stem elongation and suppresses petiole growth. We used a genome-wide transcriptome analysis to identify the molecular mechanisms underlying the observed antithetical growth responses. Though submergence caused a substantial reconfiguration of the petiole and stem transcriptome, only little qualitative differences were observed between both tissues. A core submergence response included hormonal regulation and metabolic readjustment for energy conservation, whereas tissue-specific responses were associated with defense, photosynthesis, and cell wall polysaccharides. Transcriptomic and physiological characterization suggested that the established ethylene, abscisic acid (ABA), and GA growth regulatory module for underwater elongation could not fully explain underwater growth in watercress. Petiole growth suppression is likely attributed to a cell cycle arrest. Underwater stem elongation is driven by an early decline in ABA and is not primarily mediated by ethylene or GA. An enhanced stem elongation observed in the night period was not linked to hypoxia and suggests an involvement of circadian regulation