Mycotoxins contaminating animal feed can exert toxic effects in animals and be transferred into animal products. Therefore, mycotoxin occurrence in feed should be monitored. To this end, we performed a large-scale global survey of mycotoxin contamination in feed and assessed regional differences and year-to-year variation of mycotoxin occurrence. Concentrations of aflatoxin B₁, zearalenone, fumonisins, ochratoxin A, deoxynivalenol, and T-2 toxin were analyzed in 74,821 samples of feed and feed raw materials (e.g., maize, wheat, soybean) collected from 100 countries from 2008 to 2017. In total, 88% of the samples were contaminated with at least one mycotoxin. Mycotoxin occurrence showed distinct regional trends and climate was a key determinant governing these trends. In most regions, the majority of samples complied with maximum levels and guidance values for mycotoxins in animal feed that are in effect in the European Union. However, 41.1%, 38.5%, and 20.9% of samples from South Asia, Sub-Saharan Africa, and Southeast Asia, respectively, exceeded the maximum level for aflatoxin B₁ (20 µg/kg). In several regions, mycotoxin concentrations in maize showed a pronounced year-to-year variation that could be explained by rainfall or temperature during sensitive periods of grain development. A large fraction of samples (64%) was co-contaminated with ≥ 2 mycotoxins. Most frequently observed mycotoxin mixtures were combinations of deoxynivalenol, zearalenone, and fumonisins, as well as fumonisins and aflatoxin B₁. Deoxynivalenol and zearalenone concentrations were correlated in maize and wheat. In conclusion, according to an extensive global survey, mycotoxin (co-)contamination of animal feed is common, shows regional trends, and is governed in part by climate and weather.

Modern analytical techniques can determine a multitude of fungal metabolites contaminating food and feed. In addition to known mycotoxins, for which maximum levels in food are enforced, also currently unregulated, so-called “emerging mycotoxins” were shown to occur frequently in agricultural products. The aim of this review is to critically discuss the relevance of selected emerging mycotoxins to food and feed safety. Acute and chronic toxicity as well as occurrence data are presented for enniatins, beauvericin, moniliformin, fusaproliferin, fusaric acid, culmorin, butenolide, sterigmatocystin, emodin, mycophenolic acid, alternariol, alternariol monomethyl ether, and tenuazonic acid. By far not all of the detected compounds are toxicologically relevant at their naturally occurring levels and are therefore of little or no health concern to consumers. Still, gaps in knowledge have been identified for several compounds. These gaps should be closed by the scientific community in the coming years to allow a proper risk assessment.

Nitrospira are chemolithoautotrophic nitrite-oxidizing bacteria that catalyze the second step of nitrification in most oxic habitats and are important for excess nitrogen removal from sewage in wastewater treatment plants (WWTPs). To date, little is known about their diversity and ecological niche partitioning within complex communities. In this study, the fine-scale community structure and function of Nitrospira was analyzed in two full-scale WWTPs as model ecosystems. In Nitrospira-specific 16S rRNA clone libraries retrieved from each plant, closely related phylogenetic clusters (16S rRNA identities between clusters ranged from 95.8% to 99.6%) within Nitrospira lineages I and II were found. Newly designed probes for fluorescence in situ hybridization (FISH) allowed the specific detection of several of these clusters, whose coexistence in the WWTPs was shown for prolonged periods of several years. In situ ecophysiological analyses based on FISH, relative abundance and spatial arrangement quantification, as well as microautoradiography revealed functional differences of these Nitrospira clusters regarding the preferred nitrite concentration, the utilization of formate as substrate and the spatial coaggregation with ammonia-oxidizing bacteria as symbiotic partners. Amplicon pyrosequencing of the nxrB gene, which encodes subunit beta of nitrite oxidoreductase of Nitrospira, revealed in one of the WWTPs as many as 121 species-level nxrB operational taxonomic units with highly uneven relative abundances in the amplicon library. These results show a previously unrecognized high diversity of Nitrospira in engineered systems, which is at least partially linked to niche differentiation and may have important implications for process stability.

Fluorescence in situ hybridization (FISH) with singly labeled rRNA-targeted oligonucleotide probes is widely applied for direct identification of microbes in the environment or in clinical specimens. Here we show that a replacement of singly labeled oligonucleotide probes with 5′-, 3′-doubly labeled probes at least doubles FISH signal intensity without causing specificity problems. Furthermore, Cy3-doubly labeled probes strongly increase in situ accessibility of rRNA target sites and thus provide more flexibility for probe design.

Oxidizing hydrogen in place of nitrite: Microorganisms are important drivers of Earth's nitrogen cycle. Many of the organisms responsible for mediating the reactions of one phase of nitrogen to another are thought to be ecologic specialists. Using a combination of genomic and experimental analyses, Koch et al. show that Nitrospira moscoviensis , a member of a widely distributed genus of nitrite-oxidizing bacteria, can oxidize hydrogen instead of nitrite to support growth when oxygen is present. Not only does this ecologic flexibility suggest a broader distribution of these organisms in natural settings, but they may be important in engineered environments as well. Science , this issue p. 1052

Numerous past studies have shown members of the genus Nitrospira to be the predominant nitrite-oxidizing bacteria (NOB) in nitrifying wastewater treatment plants (WWTPs). Only recently, the novel NOB ‘Candidatus Nitrotoga arctica’ was identified in permafrost soil and a close relative was enriched from activated sludge. Still, little is known about diversity, distribution and functional importance of Nitrotoga in natural and engineered ecosystems. Here we developed Nitrotoga 16S rRNA-specific PCR primers and fluorescence in situ hybridization (FISH) probes, which were applied to screen activated sludge samples from 20 full-scale WWTPs. Nitrotoga-like bacteria were detected by PCR in 11 samples and reached abundances detectable by FISH in seven sludges. They coexisted with Nitrospira in most of these WWTPs, but constituted the only detectable NOB in two systems. Quantitative FISH revealed that Nitrotoga accounted for nearly 2% of the total bacterial community in one of these plants, a number comparable to Nitrospira abundances in other WWTPs. Spatial statistics revealed that Nitrotoga coaggregated with ammonia-oxidizing bacteria, strongly supporting a functional role in nitrite oxidation. This activity was confirmed by FISH in combination with microradiography, which revealed nitrite-dependent autotrophic carbon fixation by Nitrotoga in situ. Correlation of the presence or absence with WWTP operational parameters indicated low temperatures as a main factor supporting high Nitrotoga abundances, although in incubation experiments these NOB remained active over an unexpected range of temperatures, and also at different ambient nitrite concentrations. In conclusion, this study demonstrates that Nitrotoga can be functionally important nitrite oxidizers in WWTPs and can even represent the only known NOB in engineered systems.