Diversity and origins of bacterial and archaeal viruses on sinking particles reaching the abyssal ocean

© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Luo, E., Leu, A. O., Eppley, J. M., Karl, D. M., & DeLong, E. F. Diversity and origins of bacterial and archaeal viruses on sinking particles reaching the abyssal ocean. ISME Journal, 16, : 1627–1635, https://doi.org/10.1038/s41396-022-01202-1.Sinking particles and particle-associated microbes influence global biogeochemistry through particulate matter export from the surface to the deep ocean. Despite ongoing studies of particle-associated microbes, viruses in these habitats remain largely unexplored. Whether, where, and which viruses might contribute to particle production and export remain open to investigation. In this study, we analyzed 857 virus population genomes associated with sinking particles collected over three years in sediment traps moored at 4000 m in the North Pacific Subtropical Gyre. Particle-associated viruses here were linked to cellular hosts through matches to bacterial and archaeal metagenome-assembled genome (MAG)-encoded prophages or CRISPR spacers, identifying novel viruses infecting presumptive deep-sea bacteria such as Colwellia, Moritella, and Shewanella. We also identified lytic viruses whose abundances correlated with particulate carbon flux and/or were exported from the photic to abyssal ocean, including cyanophages. Our data are consistent with some of the predicted outcomes of the viral shuttle hypothesis, and further suggest that viral lysis of both autotrophic and heterotrophic prokaryotes may play a role in carbon export. Our analyses revealed the diversity and origins of prevalent viruses found on deep-sea sinking particles and identified prospective viral groups for future investigation into processes that govern particle export in the open ocean.This project is funded by grants from the Simons Foundation (#329108 to EFD and DMK, #721223 to EFD, and #721252 to DMK) and the Gordon and Betty Moore Foundation (GBMF3777 to EFD and GBMF3794 to DMK). Partial support for EL was provided by the Natural Sciences and Engineering Research Council of Canada (PGSD3-487490-2016)

Solving the Klein-Gordon equation using Fourier spectral methods: A benchmark test for computer performance

The cubic Klein-Gordon equation is a simple but non-trivial partial differential equation whose numerical solution has the main building blocks required for the solution of many other partial differential equations. In this study, the library 2DECOMP&FFT is used in a Fourier spectral scheme to solve the Klein-Gordon equation and strong scaling of the code is examined on thirteen different machines for a problem size of 512^3. The results are useful in assessing likely performance of other parallel fast Fourier transform based programs for solving partial differential equations. The problem is chosen to be large enough to solve on a workstation, yet also of interest to solve quickly on a supercomputer, in particular for parametric studies. Unlike other high performance computing benchmarks, for this problem size, the time to solution will not be improved by simply building a bigger supercomputer.Comment: 10 page

Lateral Gene Transfer Drives Metabolic Flexibility in the Anaerobic Methane-Oxidizing Archaeal Family Methanoperedenaceae

Anaerobic oxidation of methane (AOM) is an important biological process responsible for controlling the flux of methane into the atmosphere. Members of the archaeal family Methanoperedenaceae (formerly ANME-2d) have been demonstrated to couple AOM to the reduction of nitrate, iron, and manganese. Here, comparative genomic analysis of 16 Methanoperedenaceace metagenome-assembled genomes (MAGs), recovered from diverse environments, revealed novel respiratory strategies acquired through lateral gene transfer (LGT) events from diverse archaea and bacteria. Comprehensive phylogenetic analyses suggests that LGT has allowed members of the Methanoperedenaceae to acquire genes for the oxidation of hydrogen and formate, and the reduction of arsenate, selenate and elemental sulfur. Numerous membrane-bound multi-heme c type cytochrome complexes also appear to have been laterally acquired, which may be involved in the direct transfer of electrons to metal oxides, humics and syntrophic partners

Anaerobic methane oxidation coupled to manganese reduction by members of the Methanoperedenaceae

Anaerobic oxidation of methane (AOM) is a major biological process that reduces global methane emission to the atmosphere. Anaerobic methanotrophic archaea (ANME) mediate this process through the coupling of methane oxidation to different electron acceptors, or in concert with a syntrophic bacterial partner. Recently, ANME belonging to the archaeal family Methanoperedenaceae (formerly known as ANME-2d) were shown to be capable of AOM coupled to nitrate and iron reduction. Here, a freshwater sediment bioreactor fed with methane and Mn(IV) oxides (birnessite) resulted in a microbial community dominated by two novel members of the Methanoperedenaceae, with biochemical profiling of the system demonstrating Mn(IV)-dependent AOM. Genomic and transcriptomic analyses revealed the expression of key genes involved in methane oxidation and several shared multiheme c-type cytochromes (MHCs) that were differentially expressed, indicating the likely use of different extracellular electron transfer pathways. We propose the names “Candidatus Methanoperedens manganicus” and “Candidatus Methanoperedens manganireducens” for the two newly described Methanoperedenaceae species. This study demonstrates the ability of members of the Methanoperedenaceae to couple AOM to the reduction of Mn(IV) oxides, which suggests their potential role in linking methane and manganese cycling in the environment

Lymphatic microangiopathy of the skin in systemic sclerosis

METHODS: The cutaneous capillary lymphatic system in patients with systemic sclerosis was investigated using fluorescence microlymphography. The distal upper limbs of 16 healthy controls (mean age 62.3+/-13.1 yr) and 16 patients with systemic sclerosis (mean age 58.9+/-13.6 yr) were examined and the following parameters were evaluated: (a) single lymphatic capillaries; (b) lymphatic capillary network and cutaneous backflow; (c) extension of the stained lymphatics; (d) diameter of single lymphatic capillaries. RESULTS: At the finger level, lymphatic capillaries were lacking in five patients, while they were present in all controls (P < 0.05). Extension of the stained lymphatics was increased in 11 patients (8.1+/-6.0 mm) compared to the 16 healthy controls (2.0+/-1.2 mm) (P < 0.0001). Cutaneous backflow was observed in three patients (P < 0.05). At the hand level, lymphatic network extension was significantly different between patients (3.8+/-2.4 mm) and controls (1.2+/-0.8 mm) (P < 0.01); however, no significant differences were found at the forearm level. CONCLUSION: Lesional skin in patients with systemic sclerosis exhibits evidence of lymphatic microangiopath

Analysis to efficiency discrete covering worker organ when clearing vegetable raw material

In article is executed analysis to efficiency of the functioning the cleansing equipment for different type vegetable cheese: potatoes, carrot, pommel and the other type potatoes. He is indicative of that that much of the cleansing equipment uses as worker organ abrasive put, which improvement is one of the directions of increasing to his efficiency and improvements of his field-performance data. Classical model of the motion club is considered In process of the analysis in camera of the cleansing machine. For optimization of the process peelings is installed path of the motion and is calculated corner of the flight club with cone-shaped chalice. When shaping the models is considered apart taken tuber of the potatoes. Expecting his uniform sphere and without regard influence upon it other club, have defined the path of his motion on cone-shaped chalice and corner, under which tuber flies to wall. The Corner of the slopping cone chalices 30 degrees took to horizon. Integrating equation on time, got the equation of the energy balance, from which possible select required for peelings time. The Further analysis conducted the methods of the numerical experiment in system Mathcad. Got in this experiment results allow to optimize the drawing a fixing abrasive bands, taking into consideration designed methods of the shaping for such object, as worker organs cleansing machines, technology of the intermittent fixing covering. The Following stage of modeling expected consideration of the process peelings for collection cleaned club, on which expected the separate cleaned objects (for instance, potato tubers) springy element, changing their (in flat production) hard disk united between itself springy spring. Consideration this elaborated models have allowed to install the frequencies of the free fluctuations of this system and, accordingly, moments of the osculation worker organ that in significant measure defines the topology of the abrasive covering

Enhanced magnetocaloric effect in frustrated magnets

The magnetothermodynamics of strongly frustrated classical Heisenberg antiferromagnets on kagome, garnet, and pyrochlore lattices is examined. The field induced adiabatic temperature change (dT/dH)_S is significantly larger for such systems compared to ordinary non-frustrated magnets and also exceeds the cooling rate of an ideal paramagnet in a wide range of fields. An enhancement of the magnetocaloric effect is related to presence of a macroscopic number of soft modes in frustrated magnets below the saturation field. Theoretical predictions are confirmed with extensive Monte Carlo simulations.Comment: 7 page

Ecological Memory of Historical Contamination Influences the Response of Phytoplankton Communities

Ecological memory (EM) recognizes the importance of previous stress encounters in promoting community tolerance and thereby enhances ecosystem stability, provided that gained tolerances are preserved during non-stress periods. Drawing from this concept, we hypothesized that the recruitment of tolerant species can be facilitated by imposing an initial sorting process (conditioning) during the early stages of community assembly, which should result in higher production (biomass development and photosynthetic efficiency) and stable community composition. To test this, phytoplankton resting stages were germinated from lake sediments originating from two catchments that differed in contamination history: one impacted by long-term herbicides and pesticides exposures (historically contaminated lake) from an agricultural catchment compared to a low-impacted one (near-pristine lake) from a forested catchment. Conditioning was achieved by adding an herbicide (Isoproturon, which was commonly used in the catchment of the historically contaminated lake) during germination. Afterward, the communities obtained from germination were exposed to an increasing gradient of Isoproturon. As hypothesized, upon conditioning, the phytoplankton assemblages from the historically contaminated lake were able to rapidly restore photosynthetic efficiency (p > 0.01) and became structurally (community composition) more resistant to Isoproturon. The communities of the near-pristine lake did not yield these positive effects regardless of conditioning, supporting that EM was a unique attribute of the historically stressed ecosystem. Moreover, assemblages that displayed higher structural resistance concurrently yielded lower biomass, indicating that benefits of EM in increasing structural stability may trade-off with production. Our results clearly indicate that EM can foster ecosystem stability to a recurring stressor.publishedVersio

Low field hysteresis in disordered ferromagnets

We analyze low field hysteresis close to the demagnetized state in disordered ferromagnets using the zero temperature random-field Ising model. We solve the demagnetization process exactly in one dimension and derive the Rayleigh law of hysteresis. The initial susceptibility a and the hysteretic coefficient b display a peak as a function of the disorder width. This behavior is confirmed by numerical simulations d=2,3 showing that in limit of weak disorder demagnetization is not possible and the Rayleigh law is not defined. These results are in agreement with experimental observations on nanocrystalline magnetic materials.Comment: Extended version, 18 pages, 5 figures, to appear in Phys. Rev.