Studies on similarity-based interference in subject-verb number agreement dependencies have found a consistent facilitatory effect in ungrammatical sentences but no conclusive effect in grammatical sentences. Existing models propose that interference is caused either by a faulty representation of the input (encoding-based models) or by difficulty in retrieving the subject based on cues at the verb (retrieval-based models). Neither class of model captures the observed patterns in human reading time data. We propose a new model that integrates a feature encoding mechanism into an existing cue-based retrieval model. Our model outperforms the cue-based retrieval model in explaining interference effect data from both grammatical and ungrammatical sentences. These modeling results yield a new insight into sentence processing, encoding modulates retrieval. Nouns stored in memory undergo feature distortion, which in turn affects how retrieval unfolds during dependency completion.

Studies of the speed-accuracy trade-off (SAT) have been influential in arguing for the direct-access model of retrieval in sentence processing. The direct-access model assumes that long-distance dependencies rely on a content-addressable search for the correct representation in memory. Here, we address two important weaknesses in the statistical methods standardly used for analysing SAT data. First, these methods are based on non-hierarchical modelling. We show how a hierarchical model can be fit to SAT data, and we test parameter recovery in this more conservative model. The parameters most relevant to the direct-access account cannot be accurately estimated, and we attribute this to the standard SAT model being overparameterised for the limited data available to fit it. Second, the power properties of SAT studies are unknown. We conduct a power analysis and show that inferences from null results to the null hypothesis, though commonplace in the SAT literature, may be unwarranted.

Cue-based retrieval theories of sentence processing assume that subject-verb dependencies are resolved through a content-addressable search in memory. The model assumes that multiple nouns with similar syntactic or semantic features increase dependency completion difficulty. English eyetracking data (reading) are consistent with model predictions; interestingly, a similar experiment with German --a language marking case overtly-- suggests that only syntactic features affect dependency completion difficulty. Why would German show different behavior than English? Using a computational implementation of the cue-based retrieval model and model comparison using Bayes factors, we show that the reason is systematic variation at the individual-participant level: German participants overwhelmingly give higher weighting to syntactic cues over semantic cues, whereas English participants mostly give equal weighting to syntactic and semantic cues. The richer morphosyntax of German leads to syntactic cues being favoured; if such cues are largely absent (as in English) the parser relies on both cue types equally.

The current paradigm, widely incorporated in soil biogeochemical models, is that microbial methanogenesis can only occur in anoxic habitats. In contrast, here we show clear geochemical and biological evidence for methane production in well-oxygenated soils of a freshwater wetland. A comparison of oxic to anoxic soils reveal up to ten times greater methane production and nine times more methanogenesis activity in oxygenated soils. Metagenomic and metatranscriptomic sequencing recover the first near-complete genomes for a novel methanogen species, and show acetoclastic production from this organism was the dominant methanogenesis pathway in oxygenated soils. This organism, Candidatus Methanothrix paradoxum, is prevalent across methane emitting ecosystems, suggesting a global significance. Moreover, in this wetland, we estimate that up to 80% of methane fluxes could be attributed to methanogenesis in oxygenated soils. Together, our findings challenge a widely held assumption about methanogenesis, with significant ramifications for global methane estimates and Earth system modeling.

Microbial and viral communities transform the chemistry of Earth's ecosystems, yet the specific reactions catalyzed by these biological engines are hard to decode due to the absence of a scalable, metabolically resolved, annotation software. Here, we present DRAM (Distilled and Refined Annotation of Metabolism), a framework to translate the deluge of microbiome-based genomic information into a catalog of microbial traits. To demonstrate the applicability of DRAM across metabolically diverse genomes, we evaluated DRAM performance on a defined, in silico soil community and previously published human gut metagenomes. We show that DRAM accurately assigned microbial contributions to geochemical cycles and automated the partitioning of gut microbial carbohydrate metabolism at substrate levels. DRAM-v, the viral mode of DRAM, established rules to identify virally-encoded auxiliary metabolic genes (AMGs), resulting in the metabolic categorization of thousands of putative AMGs from soils and guts. Together DRAM and DRAM-v provide critical metabolic profiling capabilities that decipher mechanisms underpinning microbiome function.