On the Origins and Control of Community Types in the Human Microbiome

Microbiome-based stratification of healthy individuals into compositional categories, referred to as "community types", holds promise for drastically improving personalized medicine. Despite this potential, the existence of community types and the degree of their distinctness have been highly debated. Here we adopted a dynamic systems approach and found that heterogeneity in the interspecific interactions or the presence of strongly interacting species is sufficient to explain community types, independent of the topology of the underlying ecological network. By controlling the presence or absence of these strongly interacting species we can steer the microbial ecosystem to any desired community type. This open-loop control strategy still holds even when the community types are not distinct but appear as dense regions within a continuous gradient. This finding can be used to develop viable therapeutic strategies for shifting the microbial composition to a healthy configurationComment: Main Text, Figures, Methods, Supplementary Figures, and Supplementary Tex

Bionota: bacterias promotoras de crecimiento de microalgas: una nueva aproximación en el tratamiento de aguas residuales

Las bacterias promotoras de crecimiento en plantas (PGPB) del género Azospirillum son conocidas porque mejo­ran el crecimiento de numerosas cosechas agrícolas; sin embargo, el presente trabajo pretende extender el uso de estas bacterias a "bacterias promotoras de crecimiento de microalgas" (MPGB) para aumentar la capacidad de las microalgas de eliminar nutrientes de aguas residuales. La inoculación deliberada de las microalgas Chlorella spp. con PGPB de origen terrestre no ha sido reportada con anterioridad, tal vez debido al origen diferente de estos dos microorganismos. Al inmovilizar de manera conjunta Chlorella vulgaris y Azospirillum brasilense Cd en esferas de alginato, se obtuvo como resultado un aumento significativo en varios parámetros de crecimiento de la microalga, como el peso fresco y seco, el número total de células, el tamaño de las colonias de microalgas dentro de la esfera, el número de organismos por colonia y la concentración de pigmentos. Además, aumenta­ron los lípidos y la variedad de ácidos grasos. La microalga combinada con la MGPB tiene una mayor capacidad de eliminar amonio y fósforo tanto en agua residual sintética como en agua residual doméstica. Actualmente se ha estado experimentando con otras PGPB (Flavobacterium sp. Azospirillum sp. y Azotobacter sp.) para propósitos acuícolas; por ejemplo aumentar el crecimiento de fitoplancton utilizado en el cultivo de carpas y estabilizar cultivos masivos de microalgas marinas utilizadas como alimento para organismos marinos, todo esto con resul­tados promisorios. Si bien el efecto de las PGPB en microorganismos acuáticos aún no ha sido suficientemente explorado, proponemos que la co-inmovilización de microalgas y bacterias promotoras de crecimiento es un medio efectivo para aumentar la población microalgal y también su capacidad de limpiar aguas residuales. Palabras clave: PGPB; microalgas; biotratamiento de aguas residuales; co-inmovilización; PGPB; micro-algae; wastewater treatment; co-immobilisedPlant growth-promoting bacteria (PGPB) from the genus Azospirillum are known to enhance the growth of numerous agricultural crops. The use of these bacteria is proposed as "micro-algae-growth promoting bacteria" (MGPB) for enhancing freshwater micro-algae Chlorella vulgaris and C. sorokiniana capadty to clean polluted water. The deliberate inoculation of Chlorella sp. with a terrestrial PGPB has not been reported prior to these studies, perhaps because of the different origin of the two micro-organisms. Chlorella spp. is not known to harbour any plant growth-promoting bacteria and Azospirillum sp. is rarely used for inoculation in aquatic environments. Co-immobilisation of C. vulgaris and A. brasilense Cd in small alginate beads resulted in significant increases in numerous micro-algae growth parameters. Dry and fresh weight, total number of cells, micro-algal cluster (colonies) size within the bead, number of micro-algal cells per cluster and micro-algal pigments levels significantly increased. Lipids and the variety of fatty adds also significantly increased, as did the combination of micro-algae. MGPB had superior capacity for removing ammonium and phosphorus from polluted synthetic and municipal wastewaters than the micro-algae by itself. Other PGPB (i.e. Flavobacterium sp. Azospirillum sp. and Azotobacter sp.) are currently being tested in aquaculture; carp farming using enhanced phytoplankton growth and stabilising mass marine micro-algae culture for use as feed for marine organisms are both retuming promising results. This aspect of PGPB effect on water micro-organisms is currently in its infancy. We pro pose that co-immobilising micro-algae and plant growth-promoting bacteria represent an effective means of increasing micro-algal populations and also their capacity for cleaning polluted water. Key words: PGPB; micro-algae; wastewater treatment; co-immobilise

Comparing the performance of FA, DFA and DMA using different synthetic long-range correlated time series

Notwithstanding the significant efforts to develop estimators of long-range correlations (LRC) and to compare their performance, no clear consensus exists on what is the best method and under which conditions. In addition, synthetic tests suggest that the performance of LRC estimators varies when using different generators of LRC time series. Here, we compare the performances of four estimators [Fluctuation Analysis (FA), Detrended Fluctuation Analysis (DFA), Backward Detrending Moving Average (BDMA), and centred Detrending Moving Average (CDMA)]. We use three different generators [Fractional Gaussian Noises, and two ways of generating Fractional Brownian Motions]. We find that CDMA has the best performance and DFA is only slightly worse in some situations, while FA performs the worst. In addition, CDMA and DFA are less sensitive to the scaling range than FA. Hence, CDMA and DFA remain "The Methods of Choice" in determining the Hurst index of time series.Comment: 6 pages (including 3 figures) + 3 supplementary figure

Long-term correlations and multifractal nature in the intertrade durations of a liquid Chinese stock and its warrant

Intertrade duration of equities is an important financial measure characterizing the trading activities, which is defined as the waiting time between successive trades of an equity. Using the ultrahigh-frequency data of a liquid Chinese stock and its associated warrant, we perform a comparative investigation of the statistical properties of their intertrade duration time series. The distributions of the two equities can be better described by the shifted power-law form than the Weibull and their scaled distributions do not collapse onto a single curve. Although the intertrade durations of the two equities have very different magnitude, their intraday patterns exhibit very similar shapes. Both detrended fluctuation analysis (DFA) and detrending moving average analysis (DMA) show that the 1-min intertrade duration time series of the two equities are strongly correlated. In addition, both multifractal detrended fluctuation analysis (MFDFA) and multifractal detrending moving average analysis (MFDMA) unveil that the 1-min intertrade durations possess multifractal nature. However, the difference between the two singularity spectra of the two equities obtained from the MFDMA is much smaller than that from the MFDFA.Comment: 10 latex pages, 4 figure

The interactive effects of arbuscular mycorrhiza and plant growth-promoting rhizobacteria synergistically enhance host plant defences against pathogens

Belowground interactions between plant roots, mycorrhizal fungi and plant growth-promoting rhizobacteria (PGPR) can improve plant health via enhanced nutrient acquisition and priming of the plant immune system. Two wheat cultivars differing in their ability to form mycorrhiza were (co)inoculated with the mycorrhizal fungus Rhizophagus irregularis and the rhizobacterial strain Pseudomonas putida KT2440. The cultivar with high mycorrhizal compatibility supported higher levels of rhizobacterial colonization than the low compatibility cultivar. Those levels were augmented by mycorrhizal infection. Conversely, rhizobacterial colonization of the low compatibility cultivar was reduced by mycorrhizal arbuscule formation. Single inoculations with R. irregularis or P. putida had differential growth effects on both cultivars. Furthermore, while both cultivars developed systemic priming of chitosan-induced callose after single inoculations with R. irregularis or P. putida, only the cultivar with high mycorrhizal compatibility showed a synergistic increase in callose responsiveness following co-inoculation with both microbes. Our results show that multilateral interactions between roots, mycorrhizal fungi and PGPR can have synergistic effects on growth and systemic priming of wheat

Root-Associated Fungal Communities in Two Populations of the Fully Mycoheterotrophic Plant Arachnitis uniflora Phil. (Corsiaceae) in Southern Chile

The microbiological interactions of the roots of non-photosynthetic plants in South America have been scarcely explored. This study analyzes culturable fungal diversity associated with the mycoheterotrophic plant Arachnitis uniflora Phil. (Corsiaceae) in southern Chile, growing in two different understoreys of native (Nothofagus-dominated) and mixed forest (native, Cupressus sempervirens, and Pinus radiata). Rhizospheric and endophytic fungi were isolated, cultured, and purified to identify microorganisms associated with A. uniflora roots. We showed the different fungi associated with the plant, and that these distributions are influenced by the sampling site. We isolated 410 fungal strains (144 endophytic and 266 from the rhizosphere). We identified 13 operative taxonomical units from plants sampled in the mixed forest, while 15 were from the native forest. Rhizospheric microorganisms were mainly related to Penicillium spp., whereas some pathogenic and saprophytic strains were more frequent inside the roots. Our results have also shown that the fungal strains are weak for phosphate solubilization, but other pathways such as organic acid exudation and indole acetic acid production can be considered as major mechanisms to stimulate plant growth. Our results point to new fungal associates of A. uniflora plants reported in Andean ecosystems, identifying new beneficial endophytic fungi associated with roots of this fully mycoheterotrophic plant.This research was funded by Fondo Nacional de Desarrollo Científico y Tecnológico (FONDECYT), grant number 1170931 to C.A. (Cesar Arriagada) and Fondo De Fomento al Desarrollo Científico y Tecnológico (FONDECYT), grant number VIU17E0185 to H.H. (Hector Herrera)

Endophytes vs tree pathogens and pests: can they be used as biological control agents to improve tree health?

Like all other plants, trees are vulnerable to attack by a multitude of pests and pathogens. Current control measures for many of these diseases are limited and relatively ineffective. Several methods, including the use of conventional synthetic agro-chemicals, are employed to reduce the impact of pests and diseases. However, because of mounting concerns about adverse effects on the environment and a variety of economic reasons, this limited management of tree diseases by chemical methods is losing ground. The use of biological control, as a more environmentally friendly alternative, is becoming increasingly popular in plant protection. This can include the deployment of soil inoculants and foliar sprays, but the increased knowledge of microbial ecology in the phytosphere, in particular phylloplane microbes and endophytes, has stimulated new thinking for biocontrol approaches. Endophytes are microbes that live within plant tissues. As such, they hold potential as biocontrol agents against plant diseases because they are able to colonize the same ecological niche favoured by many invading pathogens. However, the development and exploitation of endophytes as biocontrol agents will have to overcome numerous challenges. The optimization and improvement of strategies employed in endophyte research can contribute towards discovering effective and competent biocontrol agents. The impact of environment and plant genotype on selecting potentially beneficial and exploitable endophytes for biocontrol is poorly understood. How endophytes synergise or antagonise one another is also an important factor. This review focusses on recent research addressing the biocontrol of plant diseases and pests using endophytic fungi and bacteria, alongside the challenges and limitations encountered and how these can be overcome. We frame this review in the context of tree pests and diseases, since trees are arguably the most difficult plant species to study, work on and manage, yet they represent one of the most important organisms on Earth