Ecosystem-bedrock interaction changes nutrient compartmentalization during early oxidative weathering

Ecosystem-bedrock interactions power the biogeochemical cycles of Earth's shallow crust, supporting life, stimulating substrate transformation, and spurring evolutionary innovation. While oxidative processes have dominated half of terrestrial history, the relative contribution of the biosphere and its chemical fingerprints on Earth's developing regolith are still poorly constrained. Here, we report results from a two-year incipient weathering experiment. We found that the mass release and compartmentalization of major elements during weathering of granite, rhyolite, schist and basalt was rock-specific and regulated by ecosystem components. A tight interplay between physiological needs of different biota, mineral dissolution rates, and substrate nutrient availability resulted in intricate elemental distribution patterns. Biota accelerated CO2 mineralization over abiotic controls as ecosystem complexity increased, and significantly modified stoichiometry of mobilized elements. Microbial and fungal components inhibited element leaching (23.4% and 7%), while plants increased leaching and biomass retention by 63.4%. All biota left comparable biosignatures in the dissolved weathering products. Nevertheless, the magnitude and allocation of weathered fractions under abiotic and biotic treatments provide quantitative evidence for the role of major biosphere components in the evolution of upper continental crust, presenting critical information for large-scale biogeochemical models and for the search for stable in situ biosignatures beyond Earth.Comment: 41 pages (MS, SI and Data), 16 figures (MS and SI), 6 tables (SI and Data). Journal article manuscrip

Probabilistic models of biological enzymatic polymerization.

In this study, hierarchies of probabilistic models are evaluated for their ability to characterize the untemplated addition of adenine and uracil to the 3' ends of mitochondrial mRNAs of the human pathogen Trypanosoma brucei, and for their generative abilities to reproduce populations of these untemplated adenine/uridine "tails". We determined the most ideal Hidden Markov Models (HMMs) for this biological system. While our HMMs were not able to generatively reproduce the length distribution of the tails, they fared better in reproducing nucleotide composition aspects of the tail populations. The HMMs robustly identified distinct states of nucleotide addition that correlate to experimentally verified tail nucleotide composition differences. However they also identified a surprising subclass of tails among the ND1 gene transcript populations that is unexpected given the current idea of sequential enzymatic action of untemplated tail addition in this system. Therefore, these models can not only be utilized to reflect biological states that we already know about, they can also identify hypotheses to be experimentally tested. Finally, our HMMs supplied a way to correct a portion of the sequencing errors present in our data. Importantly, these models constitute rare simple pedagogical examples of applied bioinformatic HMMs, due to their binary emissions

Heterozygous inversion breakpoints suppress meiotic crossovers by altering recombination repair outcomes.

Heterozygous chromosome inversions suppress meiotic crossover (CO) formation within an inversion, potentially because they lead to gross chromosome rearrangements that produce inviable gametes. Interestingly, COs are also severely reduced in regions nearby but outside of inversion breakpoints even though COs in these regions do not result in rearrangements. Our mechanistic understanding of why COs are suppressed outside of inversion breakpoints is limited by a lack of data on the frequency of noncrossover gene conversions (NCOGCs) in these regions. To address this critical gap, we mapped the location and frequency of rare CO and NCOGC events that occurred outside of the dl-49 chrX inversion in D. melanogaster. We created full-sibling wildtype and inversion stocks and recovered COs and NCOGCs in the syntenic regions of both stocks, allowing us to directly compare rates and distributions of recombination events. We show that COs outside of the proximal inversion breakpoint are distributed in a distance-dependent manner, with strongest suppression near the inversion breakpoint. We find that NCOGCs occur evenly throughout the chromosome and, importantly, are not suppressed near inversion breakpoints. We propose a model in which COs are suppressed by inversion breakpoints in a distance-dependent manner through mechanisms that influence DNA double-strand break repair outcome but not double-strand break formation. We suggest that subtle changes in the synaptonemal complex and chromosome pairing might lead to unstable interhomolog interactions during recombination that permits NCOGC formation but not CO formation

S5 Fig -

A) Raw counts of CO frequencies in Oregon-RM. 96 COs between y and cv or wy and f were sequenced. COs that occur between cv and wy were from samples that had more than one CO on the chromosome. These COs were not included in any analysis. B) Raw counts of CO frequencies from dl-49 heterozygotes. 145 COs between y and f were sequenced. (DOCX)</p

Location and frequencies of NCOGCs recovered from Oregon-RM and <i>dl-49</i> heterozygotes.

Location and frequencies of NCOGCs recovered from Oregon-RM and dl-49 heterozygotes.</p

CO frequencies in <i>dl-49</i> heterozygotes from cross 1 and cross 2 (Fig 2).

These distributions are not significantly different from each other and were combined into one dataset (Kolmogorov-Smirnov test, p = 0.61). (DOCX)</p

Sequencing confirmation of pre-meiotic NCOGC events.

Table lists the location of NCOGC, primers used for PCR and sequencing, expected PCR product size, and the samples sequenced. Sanger sequencing traces are shown for each sample and are in the same order as in the table. (DOCX)</p

Fig 1 -

A) Canonical recombination pathways used in meiosis. 1) Meiosis is initiated by an enzymatically mediated DSB. 2) The DSB is resected into single-stranded ends, one of which invades the homologous chromosome and primes DNA synthesis. This forms a displacement loop (D-loop) and during synthesis dependent strand annealing (SDSA), this structure can be unwound by a helicase into a NCO. 3) If the second end of the DSB is captured by the D-loop, it also primes synthesis. 4) The second-end capture intermediate is ligated into a double Holliday Junction, which is cleaved by a meiosis-specific endonuclease to form mostly COs, although some NCOs can occasionally form. B) Predicted pairing arrangement between an inversion and a standard arrangement homologous chromosome. Single COs within the inversion breakpoints lead to acentric and dicentric chromosomes with deletions and duplications. If these COs occur, they are not recovered in the offspring (the so-called transmission distortion effect). COs are also suppressed in the collinear regions outside of the inversion breakpoints, even though COs in these regions would not lead to chromosome rearrangements. This suggests that COs are prevented from forming, as opposed to being suppressed due to transmission distortion.</p