Resource-allocation constraint governs structure and function of microbial communities in metabolic modeling

Predictive modeling tools for assessing microbial communities are important for realizing transformative capabilities of microbiomes in agriculture, ecology, and medicine. Constraint-based community-scale metabolic modeling is unique in its potential for making mechanistic predictions regarding both the structure and function of microbial communities. However, accessing this potential requires an understanding of key physicochemical constraints, which are typically considered on a per-species basis. What is needed is a means of incorporating global constraints relevant to microbial ecology into community models. Resource-allocation constraint, which describes how limited resources should be distributed to different cellular processes, sets limits on the efficiency of metabolic and ecological processes. In this study, we investigate the implications of resource-allocation constraints in community-scale metabolic modeling through a simple mechanism-agnostic implementation of resource-allocation constraints directly at the flux level. By systematically performing single-, two-, and multi-species growth simulations, we show that resource-allocation constraints are indispensable for predicting the structure and function of microbial communities. Our findings call for a scalable workflow for implementing a mechanistic version of resource-allocation constraints to ultimately harness the full potential of community-scale metabolic modeling tools.     

Organic waste conversion through anaerobic digestion: A critical insight into the metabolic pathways and microbial interactions

Anaerobic digestion is a promising method for energy recovery through conversion of organic waste to biogas and other industrial valuables. However, to tap the full potential of anaerobic digestion, deciphering the microbial metabolic pathway activities and their underlying bioenergetics is required. In addition, the behavior of organisms in consortia along with the analytical abilities to kinetically measure their metabolic interactions will allow rational optimization of the process. This review aims to explore the metabolic bottlenecks of the microbial communities adopting latest advances of profiling and ¹³C tracer-based analysis using state of the art analytical platforms (GC, GC-MS, LC-MS, NMR). The review summarizes the phases of anaerobic digestion, the role of microbial communities, key process parameters of significance, syntrophic microbial interactions and the bottlenecks that are critical for optimal bioenergetics and enhanced production of valuables. Considerations into the designing of efficient synthetic microbial communities as well as the latest advances in capturing their metabolic cross talk will be highlighted. The review further explores how the presence of additives and inhibiting factors affect the metabolic pathways. The critical insight into the reaction mechanism covered in this review may be helpful to optimize and upgrade the anaerobic digestion system.     

Characterization of the gut microbiome in the beet armyworm Spodoptera exigua in response to the short-term thermal stress

The gut microbiota is critical for energy and nutrient utilization and plays a role in host immunity in response to environmental changes. The beet armyworm Spodoptera exigua is a worldwide polyphagous agricultural pest and has frequently experienced potentially stressful temperature fluctuations under natural environmental conditions. However, little is known about the effects of thermal stress on the gut microbiome of this moth pest. Therefore, we investigated the gut microbiome variations, composition and community structure of S. exigua among low-temperature (10 °C), control (26 °C) and high temperature (35 °C) treatments using 16S amplicon sequencing. Overall, 1,192,707 high-quality reads and 762 operational taxonomic units (OTUs) were detected from 15 samples. A total of 289 genera belonging to 19 bacterial phyla were captured, with Firmicutes and Proteobacteria being the most prominent phyla. Alpha diversity metrics indicated no significant differences in the gut bacterial diversity of S. exigua among the three temperature treatments. Principal coordinates and hierarchical cluster analysis revealed significant differences in the structure of gut microbiota between the low-temperature treatment and the other two temperature treatments. In addition, PICRUSt2 analysis demonstrated that the predicted metagenomes associated with the gut microbiome were amino carbohydrate transport and metabolism, acid transport and metabolism, inorganic ion transport and metabolism and cellular processes. Our study showed that thermal stress induced changes in the gut microbiome of the beet armyworm, which may contribute to better understanding the ecological adaptation of S. exigua under changing temperature trends and to evaluating the use of gut microorganisms as biocontrol agents for this pest.     

Connectivity with primary forest determines the value of secondary tropical forests for bird conservation

Species extinctions caused by the destruction and degradation of tropical primary forest may be at least partially mitigated by the expansion of regenerating secondary forest. However, the conservation value of secondary forest remains controversial, and potentially underestimated, since most previous studies have focused on young, single‐aged, or isolated stands. Here, we use point‐count surveys to compare tropical forest bird communities in 20–120‐year‐old secondary forest with primary forest stands in central Panama, with varying connectivity between secondary forest sites and extensive primary forest. We found that species richness and other metrics of ecological diversity, as well as the combined population density of all birds, reached a peak in younger (20‐year‐old) secondary forests and appeared to decline in older secondary forest stands. This counter‐intuitive result can be explained by the greater connectivity between younger secondary forests and extensive primary forests at our study site, compared with older secondary forests that are either (a) more isolated or (b) connected to primary forests that are themselves small and isolated. Our results suggest that connectivity with extensive primary forest is a more important determinant of avian species richness and community structure than forest age, and highlight the vital contribution secondary forests can make in conserving tropical bird diversity, so long as extensive primary habitats are adjacent and spatially connected.Abstract in Spanish is available with online material.     

The nanotechnology among US: are metal and metal oxides nanoparticles a nano or mega risk for soil microbial communities?

Metal nanoparticles and metal oxides nanoparticles (MNPs/MONPs) have been widely included in a great diversity of products and industrial applications and they are already a part of our everyday life. According to estimation studies, their production is expected to increase exponentially in the next few years. Consequently, soil has been suggested as the main sink of MNPs/MONPs once they are deliberately or accidentally released into the environment. The potential negative perturbations that may result on soil microbial communities and ecological processes are resulting in concerns. Several nano-toxicological studies of MNPs/MONPs, reported so far, have focused on aquatic organisms, animals, and soil invertebrates. However, during recent years, the studies have been oriented to understand the effects of MNPs/MONPs on microbial communities and their interaction with soil components. The studies have suggested that MNPs/MONPs are one of the most toxic type to soil biota, amongst different types of nanomaterials. This may threaten soil health and fertility, since microbial communities are known to support important biological processes and ecosystem services such as the nutrient cycling, whereby their protection against the environmental pollution is imperative. Therefore, in this review we summarize the actual knowledge available from the last five years (2013–2018) and gaps about the potential negative, positive or neutral effects produced on soil by different classes of MNPs/MONPs. A particular emphasis has been placed on the associated soil microorganisms and biological processes. Finally, perspectives about future research are discussed.     

Microbial mats and physicochemistry in a saltern in the Bretagne (France) and in a laboratory scale saltern model

Abstract A saltern near La Baule (Bretagne, France) was remodeled in a programmable temperature and humidity controlled walk-in environmental chamber resembling the characteristics of the original saltern. The saltern showed different types of microbial mats predominantly composed of algae, oxy- and anoxyphotobacteria, and associated chemoorganotrophic bacteria, fungi and animals. Well-developed microbial mats were found up to a salinity of 10% during the three or four months in summer when salinity gradients and NaCl precipitation were established. The main phototrophic organisms were diatoms, the cyanobacteria Aphanothece, Microcoleus, Spirulina , and Oscillatoria , and Chromatiaceae. At higher salinity, Halobacterium sp., diatoms, and Dunaliella were dominant. Typical microbial mats and saltern-typical invertebrate, algal and bacterial species also developed in the saltern model, building up a stable community. The ionic composition of the brines and physicochemical parameters were similar to those determined for the original saltern. Different photosynthetic organisms, e.g. a filamentous purple bacterium and a hypersaline Chloroflexus -like organism, could be enriched within the microbial mats by changing the light regime.     

The ecology of the sandy estuaries of North Devon and Carmarthen Bay

The estuaries of the Taf, Tywi, Gwendraeth and Loughor (Carmarthen Bay, South Wales), and the Taw and Torridge (North Devon) were surveyed during the spring and summer of 1988, as part of a four year study of harbours, rias and estuaries in southern Britain commissioned by the Nature Conservancy Council. The aims of these surveys were to describe the major marine habitats and communities present in each estuary, and to assess their nature conservation importance. This paper outlines the results of these surveys, concentrating on the many environmental similarities between the six estuaries.     

Tropical dry forest trees and the relationship between local abundance and geographic range

Aim To test the macroecological principle that a positive relationship exists between local abundance and geographic range size for tree communities in the tropical dry forest. Location Two tropical dry forest (TDF) regions on the Pacific coast of Mexico: one near Chamela, Jalisco; the other near Huatulco, Oaxaca. Methods We recorded species presence and relative abundance of trees and lianas from over 40 locales in each of the study regions using transects across an elevational gradient. We then compared the field data with occurrence data from national and online databases to examine how local patterns of abundance relate to putative geographic range areas and latitudinal breadth. Results We found no significant correlation between abundance and range size. Overall, many more locally abundant species had small ranges than large ones. We found that most species occupy the majority of the TDF range north of Colombia, and those species present in South America occupy the majority of that continent’s TDF range as well. This pattern was independent of local abundance. We also found no relationship between range size and local niche breadth as measured by elevation, or between local abundance and distance to the range centre. Main conclusions The macroecological tenet that posits a positive correlation between local abundance and geographic range size does not appear to hold for TDF trees. The finding that many locally abundant species had narrow ranges also suggests that dry forest endemics may be particularly well adapted to local conditions and make important contributions to community structure. We hypothesize that the absence of abundant species with large ranges is due to opposing environmental constraints that prevent a species from thriving everywhere.     

Modeling Sustainability of Arctic Communities: An Interdisciplinary Collaboration of Researchers and Local Knowledge Holders

How will climate change affect the sustainability of Arctic villages over the next 40 years? This question motivated a collaboration of 23 researchers and four Arctic communities (Old Crow, Yukon Territory, Canada; Aklavik, Northwest Territories, Canada; Fort McPherson, Northwest Territories, Canada; and Arctic Village, Alaska, USA) in or near the range of the Porcupine Caribou Herd. We drew on existing research and local knowledge to examine potential effects of climate change, petroleum development, tourism, and government spending cutbacks on the sustainability of four Arctic villages. We used data across eight disciplines to develop an Arctic Community Synthesis Model and a Web-based, interactive Possible Futures Model. Results suggested that climate warming will increase vegetation biomass within the herd’s summer range. However, despite forage increasing, the herd was projected as likely to decline with a warming climate because of increased insect harassment in the summer and potentially greater winter snow depths. There was a strong negative correlation between hypothetical, development-induced displacement of cows and calves from utilized calving grounds and calf survival during June. The results suggested that climate warming coupled with petroleum development would cause a decline in caribou harvest by local communities. Because the Synthesis Model inherits uncertainties associated with each component model, sensitivity analysis is required. Scientists and stakeholders agreed that (1) although simulation models are incomplete abstractions of the real world, they helped bring scientific and community knowledge together, and (2) relationships established across disciplines and between scientists and communities were a valuable outcome of the study. Additional project materials, including the Web-based Possible Futures Model, are available at http://www.taiga.net/sustain.