Seeing the forest for the genes: using metagenomics to infer the aggregated traits of microbial communities

Most environments harbor large numbers of microbial taxa with ecologies that remain poorly described and characterizing the functional capabilities of whole communities remains a key challenge in microbial ecology. Shotgun metagenomic analyses are increasingly recognized as a powerful tool to understand community-level attributes. However, much of this data is under-utilized due, in part, to a lack of conceptual strategies for linking the metagenomic data to the most relevant community-level characteristics. Microbial ecologists could benefit by borrowing the concept of community-aggregated traits (CATs) from plant ecologists to glean more insight from the ever-increasing amount of metagenomic data being generated. CATs can be used to quantify the mean and variance of functional traits found in a given community. A CAT-based strategy will often yield far more useful information for predicting the functional attributes of diverse microbial communities and changes in those attributes than the more commonly used analytical strategies. A more careful consideration of what CATs to measure and how they can be quantified from metagenomic data, will help build a more integrated understanding of complex microbial communities

Blind Symbol Rate Estimation of Faster-than-Nyquist Signals Based on Higher-Order Statistics

Both faster-than-Nyquist (FTN) and cognitive radio go towards an efficient use of spectrum in radio communications systems at the cost of an added computational complexity at the receiver side. To gain the maximum potential from these techniques, non-data-aided receivers are of interest. In this paper, we use fourth-order statistics to perform blind symbol rate estimation of FTN signals. The estimator shows good performance results for moderate system's densities beyond the Nyquist rate and for a reasonable number of received samples

Estudi d'un emissor-receptor faster-than-Nyquist de baixa complexitat per a les comunicacions per satèl·lit

Transmissor/receiver for ACARS systemCapacity increase in satelite communications systems is nowadays a main concern. In order to increase the spectral efficiency of such systems, a research topic consists in specifying non-orthogonal modulations called faster-than-Nyquist (FTN). By means of this technique, a capacity increase could be obtained at the cost of more complexity at the receiver side. The FTN system design consists in using pulse shaping and equalizing techniques such that a good compromise is obtained between spectal efficiency, level of interference and complexity. Within the frame of Direct-to-Home (DTH) satellite broadcast or mobile terminals, complexity becomes the main limiting factor in order to ensure low cost user terminal integration.El aumento de la capacidad de los sistemas de transmisión por satélite se encuentra en el centro de las preocupaciones actuales. Con el objetivo de augmentar la eficacidad espectral de tales sistemas, un tema de estudio consiste en especificar modulaciones no ortogonales llamadas faster-than-Nyquist (FTN). Con el uso de esta técnica, se podria augmentar la capacidad de los sistemas de transmisión a cambio de aumentar la complejidad de los receptores. El diseño de un sistema FTN consiste en determinar una estrategia de filtrado y de ecualización permitiendo un buen compromiso entre eficacidad espectral, nivel de interferencia y complejidad. En el contexto de difusión por satélite Direct-to-Home (DTH) o en el caso de terminales móviles, la limitación de complejidad es fundamental para garantizar la integración a bajo coste en los terminales de usuario.L'augment de la capacitat dels sistemes de transmissió per satèl·lit es troba al centre de les preocupacions actuals. Amb l'objectiu d'augmentar l'eficacitat espectral d'aquests sistemes, un eix de recerca consisteix en especificar modulacions no ortogonals anomenades faster-than-Nyquist (FTN). Utilitzant aquesta tècnica, es podria augmentar la capacitat dels sistemes de transmissió a canvi d'augmentar la complexitat dels receptors. El disseny d'un sistema FTN consisteix en determinar una estratègia de filtratge i d'equalització permetent un bon compromis entre eficacitat espectral, nivell d'interferència i complexitat. En el contexte de difusió per satèl ·lit Direct-to-Home (DTH) o en el cas de terminals mòbils, la limitació de complexitat és fonamental per garantir l'integració a baix cost als terminals d'usuari

Closed-Form Expressions for Channel Shortening Receivers Using A Priori Information

Channel shortening has been studied in the context of ISI and MIMO channels as a means to compute a posteriori probabilities with a BCJR algorithm at a reduced computational complexity. This is done by considering an approximate channel response of reduced length. In a turbo receiver, soft a priori information can be linearly combined with the received sequence to form a new input to the BCJR trellis-based processing. In this letter, we provide closed-form expressions for the channel shortening filters using a generalized mutual information objective function. The proposed receiver allows a complexity reduction with respect to numerical optimization approaches which may also present stability, precision and convergence issues

On zero-forcing equalization for short-filtered multicarrier faster-than-Nyquist signaling

Within the context of faster-than-Nyquist signaling, a low-complexity multicarrier system based on short-length filters and zero-forcing turbo equalization is introduced. Short-length filters allow a reduced-size block processing while zero-forcing equalization allows a linear reduced-complexity implementation. Furthermore, rectangular and out-of-band energy minimization pulse shaping demonstrates competitive performance results over an additive white Gaussian noise channel while keeping a lower computational cost than other multicarrier faster-than-Nyquist systems

Faster-than-Nyquist Signaling: on Linear and Non-Linear Reduced-Complexity Turbo Equalization

In the framework of digital video broadcasting by satellite - second generation (DVB-S2), we analyze a faster-than-Nyquist (FTN) system based on turbo equalization and low-density parity-check (LDPC) codes. Truncated maximum a posteriori (MAP) and minimum mean square error (MMSE) equalizers provide a reduced-complexity implementation of the FTN system. On the other hand, LDPC codes allow us to demonstrate attractive performance results over an additive white Gaussian noise (AWGN) channel while increasing spectral efficiency beyond the Nyquist rate and keeping a complexity comparable to that of a current DVB-S2 mode

Using network analysis to explore co-ocurrence patterns in soil microbial communities.

9 páginas, 1 tabla, 4 figuras.Exploring large environmental datasets generated by high-throughput DNA sequencing technologies requires new analytical approaches to move beyond the basic inventory descriptions of the composition and diversity of natural microbial communities. In order to investigate potential interactions between microbial taxa, network analysis of significant taxon co-occurrence patterns may help to decipher the structure of complex microbial communities across spatial or temporal gradients. Here, we calculated associations between microbial taxa and applied network analysis approaches to a 16S rRNA gene barcoded pyrosequencing dataset containing >160 000 bacterial and archaeal sequences from 151 soil samples from a broad range of ecosystem types. We described the topology of the resulting network and defined operational taxonomic unit categories based on abundance and occupancy (that is, habitat generalists and habitat specialists). Co-occurrence patterns were readily revealed, including general non-random association, common life history strategies at broad taxonomic levels and unexpected relationships between community members. Overall, we demonstrated the potential of exploring inter-taxa correlations to gain a more integrated understanding of microbial community structure and the ecological rules guiding community assembly.AB is supported by the Spanish FPU predoctoral scholarship program and EOC by grants PIRENA CGL2009-13318 and CONSOLIDER-INGENIO 2010 GRACCIE CSD2007-00067 from the Spanish Ministerio de Ciencia e Innovacio´n (MICINN).Peer reviewe

Geographical Distribution of Fungal Plant Pathogens in Dust Across the United States

As the world's population grows, global food production will need to increase. While food production efficiency has increased in recent decades through pathogen control, climate change poses new challenges in crop protection against pathogens. Understanding the natural geographical distribution and dispersal likelihood of fungal plant pathogens is essential for forecasting disease plant spread. Here we used cultivation-independent techniques to identify fungal plant pathogens in 1,289 near-surface dust samples collected across the United States. We found that overall fungal pathogen community composition is more related to environmental conditions (in particular soil pH, precipitation and frost) than to agricultural hosts and practices. We also delimited five susceptibility geographical areas in the United States where different sets of pathogens tend to occur.Open access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Seasonal niche differentiation among closely related marine bacteria

Bacteria display dynamic abundance fluctuations over time in marine environments, where they play key biogeochemical roles. Here, we characterized the seasonal dynamics of marine bacteria in a coastal oligotrophic time series station, tested how similar the temporal niche of closely related taxa is, and what are the environmental parameters modulating their seasonal abundance patterns. We further explored how conserved the niche is at higher taxonomic levels. The community presented recurrent patterns of seasonality for 297 out of 6825 amplicon sequence variants (ASVs), which constituted almost half of the total relative abundance (47%). For certain genera, niche similarity decreased as nucleotide divergence in the 16S rRNA gene increased, a pattern compatible with the selection of similar taxa through environmental filtering. Additionally, we observed evidence of seasonal differentiation within various genera as seen by the distinct seasonal patterns of closely related taxa. At broader taxonomic levels, coherent seasonal trends did not exist at the class level, while the order and family ranks depended on the patterns that existed at the genus level. This study identifies the coexistence of closely related taxa for some bacterial groups and seasonal differentiation for others in a coastal marine environment subjected to a strong seasonality.En prensa8,95