Exploration of social spreading reveals behavior is prevalent among Pedobacter and P. fluorescens isolates, and shows variations in induction of phenotype

Within soil, bacteria are found in multi-species communities, where interactions can lead to emergent community properties. Studying bacteria in a social context is critical for investigation of community-level functions. We previously showed that co-cultured Pseudomonas fluorescens Pf0-1 and Pedobacter sp. V48 engage in interspecies social spreading (ISS) on a hard agar surface, a behavior which required close contact and depended on the nutritional environment. Here, we investigate whether social spreading is widespread among P. fluorescens and Pedobacter isolates, and whether the requirements for interaction vary. We find that this phenotype is not restricted to the interaction between P. fluorescens Pf0-1 and Pedobacter sp. V48, but is a prevalent behavior found in one clade in the P. fluorescens group and two clades in the Pedobacter genus. We show that the interaction with certain Pedobacter isolates occurred without close contact, indicating induction of spreading by a putative diffusible signal. As with ISS by Pf0-1+V48, motility of interacting pairs is influenced by the environment, with no spreading behaviors (or induction of motility) observed under high nutrient conditions. While Pf0-1+V48 require low nutrient but high NaCl conditions, in the broader range of interacting pairs the high salt influence was variable. The prevalence of motility phenotypes observed here and found within the literature indicates that community-induced locomotion in general, and social spreading in particular, is likely important within the environment. It is crucial that we continue to study microbial interactions and their emergent properties to gain a fuller understanding of the functions of microbial communities. Importance Interspecies social spreading (ISS) is an emergent behavior observed when P. fluorescens Pf0-1 and Pedobacter sp. V48 interact, during which both species move together across a surface. Importantly, this environment does not permit movement of either individual species. This group behavior suggests that communities of microbes can function in ways not predictable by knowledge of the individual members. Here we have asked whether ISS is widespread and thus potentially of importance in soil microbial communities. The significance of this research is the demonstration that surface spreading behaviors are not unique to the Pf0-1-V48 interaction, but rather is a more widespread phenomenon observed among members of distinct clades of both P. fluorescens and Pedobacter isolates. Further, we identify differences in mechanism of signaling and nutritional requirements for ISS. Emergent traits resulting from bacterial interactions are widespread and their characterization is necessary for a complete understanding of microbial community function.

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Exploration of social spreading reveals behavior is prevalent among Pedobacter and P. fluorescens isolates, and shows variations in induction of phenotype

10.1101/758656 ◽

2019 ◽

Author(s):

Lucy M. McCully ◽

Jasmine Graslie ◽

Adam S. Bitzer ◽

Auður M. Sigurbjörnsdóttir ◽

Oddur Vilhelmsson ◽

...

Keyword(s):

Social Context ◽

Microbial Communities ◽

Soil Bacteria ◽

Close Contact ◽

Microbial Interactions ◽

Emergent Properties ◽

High Nutrient ◽

Agar Surface ◽

Nutritional Environment ◽

Emergent Community

AbstractWithin soil, bacteria are naturally found in multi-species communities, where interactions can lead to emergent community properties. It is critical that we study bacteria in a social context to investigate community-level functions. We previously showed that when co-cultured, Pseudomonas fluorescens Pf0-1 and Pedobacter sp. V48 engage in interspecies social spreading on a hard agar surface, a behavior which required close contact and was dependent on the nutritional environment. In this study, we investigate whether the ability to participate in social spreading is widespread among P. fluorescens and Pedobacter isolates, and whether the requirements for interaction vary. We find that this phenotype is not restricted to the interaction between P. fluorescens Pf0-1 and Pedobacter sp. V48, but is a more prevalent behavior found in one clade in the P. fluorescens group and two clades in the Pedobacter genus. We also discovered that the interaction with certain Pedobacter isolates occurred without close contact, indicating induction of spreading by a putative diffusible signal. As is the case for ISS by Pf0-1+V48, motility of all interacting pairs is influenced by the environment, with no spreading behaviors observed under high nutrient conditions. While Pf0-1+V48 require low nutrient but high NaCl conditions, in the broader range of interacting pairs this requirement for low nutrient and high salt was variable. The prevalence of motility phenotypes observed in this study and found within the literature indicates that community-induced locomotion in general, and social spreading in particular, is likely important within the environment. It is crucial that we continue to study microbial interactions and their emergent properties to gain a fuller understanding of the functions of microbial communities.

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Deciphering the evolution of microbial interactions: in silico studies of two-member microbial communities

10.1101/2022.01.14.476316 ◽

2022 ◽

Author(s):

Gayathri Sambamoorthy ◽

Karthik Raman

Keyword(s):

Microbial Communities ◽

In Silico ◽

Microbial Interactions ◽

Interaction Patterns ◽

Wild Type ◽

Community Function ◽

Evolutionary Forces ◽

In Silico Studies ◽

Wide Range ◽

In The Wild

Microbes thrive in communities, embedded in a complex web of interactions. These interactions, particularly metabolic interactions, play a crucial role in maintaining the community structure and function. As the organisms thrive and evolve, a variety of evolutionary processes alter the interactions among the organisms in the community, although the community function remains intact. In this work, we simulate the evolution of two-member microbial communities in silico to study how evolutionary forces can shape the interactions between organisms. We employ genomescale metabolic models of organisms from the human gut, which exhibit a range of interaction patterns, from mutualism to parasitism. We observe that the evolution of microbial interactions varies depending upon the starting interaction and also on the metabolic capabilities of the organisms in the community. We find that evolutionary constraints play a significant role in shaping the dependencies of organisms in the community. Evolution of microbial communities yields fitness benefits in only a small fraction of the communities, and is also dependent on the interaction type of the wild-type communities. The metabolites cross-fed in the wild-type communities appear in only less than 50% of the evolved communities. A wide range of new metabolites are cross-fed as the communities evolve. Further, the dynamics of microbial interactions are not specific to the interaction of the wild-type community but vary depending on the organisms present in the community. Our approach of evolving microbial communities in silico provides an exciting glimpse of the dynamics of microbial interactions and offers several avenues for future investigations.

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Microbial Interactions in Oral Communities Mediate Emergent Biofilm Properties

Journal of Dental Research ◽

10.1177/0022034519880157 ◽

2019 ◽

Vol 99 (1) ◽

pp. 18-25 ◽

Cited By ~ 10

Author(s):

P.I. Diaz ◽

A.M. Valm

Keyword(s):

Large Scale ◽

Taxonomic Composition ◽

Cell Interactions ◽

Microbial Interactions ◽

Spatial Proximity ◽

Individual Species ◽

Emergent Properties ◽

Oral Diseases ◽

Metabolic Cooperation ◽

Cell Cell

Oral microbial communities are extraordinarily complex in taxonomic composition and comprise interdependent biological systems. The bacteria, archaea, fungi, and viruses that thrive within these communities engage in extensive cell-cell interactions, which are both beneficial and antagonistic. Direct physical interactions among individual cells mediate large-scale architectural biofilm arrangements and provide spatial proximity for chemical communication and metabolic cooperation. In this review, we summarize recent work in identifying specific molecular components that mediate cell-cell interactions and describe metabolic interactions, such as cross-feeding and exchange of electron acceptors and small molecules, that modify the growth and virulence of individual species. We argue, however, that although pairwise interaction models have provided useful information, complex community-like systems are needed to study the properties of oral communities. The networks of multiple synergistic and antagonistic interactions within oral biofilms give rise to the emergent properties of persistence, stability, and long-range spatial structure, with these properties mediating the dysbiotic transitions from health to oral diseases. A better understanding of the fundamental properties of interspecies networks will lead to the development of effective strategies to manipulate oral communities.

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Need for Laboratory Ecosystems To Unravel the Structures and Functions of Soil Microbial Communities Mediated by Chemistry

mBio ◽

10.1128/mbio.01175-18 ◽

2018 ◽

Vol 9 (4) ◽

Cited By ~ 13

Author(s):

Kateryna Zhalnina ◽

Karsten Zengler ◽

Dianne Newman ◽

Trent R. Northen

Keyword(s):

Microbial Communities ◽

Metabolic Networks ◽

Soil Microbial Communities ◽

Microbial Interactions ◽

Microbial Consortia ◽

Cellular Biology ◽

Model Organisms ◽

Soil Microbial ◽

Integrative Framework ◽

Genome Annotations

ABSTRACTThe chemistry underpinning microbial interactions provides an integrative framework for linking the activities of individual microbes, microbial communities, plants, and their environments. Currently, we know very little about the functions of genes and metabolites within these communities because genome annotations and functions are derived from the minority of microbes that have been propagated in the laboratory. Yet the diversity, complexity, inaccessibility, and irreproducibility of native microbial consortia limit our ability to interpret chemical signaling and map metabolic networks. In this perspective, we contend that standardized laboratory ecosystems are needed to dissect the chemistry of soil microbiomes. We argue that dissemination and application of standardized laboratory ecosystems will be transformative for the field, much like how model organisms have played critical roles in advancing biochemistry and molecular and cellular biology. Community consensus on fabricated ecosystems (“EcoFABs”) along with protocols and data standards will integrate efforts and enable rapid improvements in our understanding of the biochemical ecology of microbial communities.

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Contrasting effects of ammonium and nitrate additions on the biomass of soil microbial communities and enzyme activities in subtropical China

Biogeosciences ◽

10.5194/bg-14-4815-2017 ◽

2017 ◽

Vol 14 (20) ◽

pp. 4815-4827 ◽

Cited By ~ 14

Author(s):

Chuang Zhang ◽

Xin-Yu Zhang ◽

Hong-Tao Zou ◽

Liang Kou ◽

Yang Yang ◽

...

Keyword(s):

Microbial Communities ◽

Soil Ph ◽

Enzyme Activities ◽

Mycorrhizal Fungi ◽

Soil Microbial Communities ◽

Arbuscular Mycorrhizal ◽

Inhibitory Effects ◽

Total N ◽

Soil Microbial ◽

The Individual

Abstract. The nitrate to ammonium ratios in nitrogen (N) compounds in wet atmospheric deposits have increased over the recent past, which is a cause for some concern as the individual effects of nitrate and ammonium deposition on the biomass of different soil microbial communities and enzyme activities are still poorly defined. We established a field experiment and applied ammonium (NH4Cl) and nitrate (NaNO3) at monthly intervals over a period of 4 years. We collected soil samples from the ammonium and nitrate treatments and control plots in three different seasons, namely spring, summer, and fall, to evaluate the how the biomass of different soil microbial communities and enzyme activities responded to the ammonium (NH4Cl) and nitrate (NaNO3) applications. Our results showed that the total contents of phospholipid fatty acids (PLFAs) decreased by 24 and 11 % in the ammonium and nitrate treatments, respectively. The inhibitory effects of ammonium on Gram-positive bacteria (G+) and bacteria, fungi, actinomycetes, and arbuscular mycorrhizal fungi (AMF) PLFA contents ranged from 14 to 40 % across the three seasons. We also observed that the absolute activities of C, N, and P hydrolyses and oxidases were inhibited by ammonium and nitrate, but that nitrate had stronger inhibitory effects on the activities of acid phosphatase (AP) than ammonium. The activities of N-acquisition specific enzymes (enzyme activities normalized by total PLFA contents) were about 21 and 43 % lower in the ammonium and nitrate treatments than in the control, respectively. However, the activities of P-acquisition specific enzymes were about 19 % higher in the ammonium treatment than in the control. Using redundancy analysis (RDA), we found that the measured C, N, and P hydrolysis and polyphenol oxidase (PPO) activities were positively correlated with the soil pH and ammonium contents, but were negatively correlated with the nitrate contents. The PLFA biomarker contents were positively correlated with soil pH, soil organic carbon (SOC), and total N contents, but were negatively correlated with the ammonium contents. The soil enzyme activities varied seasonally, and were highest in March and lowest in October. In contrast, the contents of the microbial PLFA biomarkers were higher in October than in March and June. Ammonium may inhibit the contents of PLFA biomarkers more strongly than nitrate because of acidification. This study has provided useful information about the effects of ammonium and nitrate on soil microbial communities and enzyme activities.

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Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products

10.7287/peerj.preprints.260v1 ◽

2014 ◽

Author(s):

Christopher W. Beitel ◽

Lutz Froenicke ◽

Jenna M. Lang ◽

Ian F. Korf ◽

Richard W. Michelmore ◽

...

Keyword(s):

Microbial Communities ◽

Dna Sequences ◽

Genome Structure ◽

Three Dimensional ◽

Individual Species ◽

Mobile Dna ◽

Sequencing Data ◽

Scale Population ◽

Metagenome Assembly ◽

The Individual

Metagenomics is a valuable tool for the study of microbial communities but has been limited by the difficulty of “binning” the resulting sequences into groups corresponding to the individual species and strains that constitute the community. Moreover, there are presently no methods to track the flow of mobile DNA elements such as plasmids through communities or to determine which of these are co-localized within the same cell. We address these limitations by applying Hi-C, a technology originally designed for the study of three-dimensional genome structure in eukaryotes, to measure the cellular co-localization of DNA sequences. We leveraged Hi-C data generated from a synthetic metagenome sample to accurately cluster metagenome assembly contigs into groups that contain nearly complete genomes of each species. The Hi-C data also reliably associated plasmids with the chromosomes of their host and with each other. We further demonstrated that Hi-C data provides a long-range signal of strain-specific genotypes, indicating such data may be useful for high-resolution genotyping of microbial populations. Our work demonstrates that Hi-C sequencing data provide valuable information for metagenome analyses that are not currently obtainable by other methods. This metagenomic Hi-C method could facilitate future studies of the fine-scale population structure of microbes, as well as studies of how antibiotic resistance plasmids (or other genetic elements) mobilize in microbial communities. The method is not limited to microbiology; the genetic architecture of other heterogeneous populations of cells could also be studied with this technique.

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Sharing vitamins: Cobamides unveil microbial interactions

Science ◽

10.1126/science.aba0165 ◽

2020 ◽

Vol 369 (6499) ◽

pp. eaba0165 ◽

Cited By ~ 9

Author(s):

Olga M. Sokolovskaya ◽

Amanda N. Shelton ◽

Michiko E. Taga

Keyword(s):

Microbial Communities ◽

Microbial Interactions ◽

Individual Species ◽

Vitamin B ◽

Complete Understanding ◽

Metabolic Functions ◽

The Family ◽

Enzyme Cofactors

Microbial communities are essential to fundamental processes on Earth. Underlying the compositions and functions of these communities are nutritional interdependencies among individual species. One class of nutrients, cobamides (the family of enzyme cofactors that includes vitamin B12), is widely used for a variety of microbial metabolic functions, but these structurally diverse cofactors are synthesized by only a subset of bacteria and archaea. Advances at different scales of study—from individual isolates, to synthetic consortia, to complex communities—have led to an improved understanding of cobamide sharing. Here, we discuss how cobamides affect microbes at each of these three scales and how integrating different approaches leads to a more complete understanding of microbial interactions.

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Rhizosphere Microbial Community Dynamics in Glyphosate-Treated Susceptible and Resistant Biotypes of Giant Ragweed (Ambrosia trifida)

Weed Science ◽

10.1614/ws-d-13-00164.1 ◽

2014 ◽

Vol 62 (2) ◽

pp. 370-381 ◽

Cited By ~ 8

Author(s):

Jessica R. Schafer ◽

Steven G. Hallett ◽

William G. Johnson

Keyword(s):

Microbial Community ◽

Next Generation Sequencing ◽

Microbial Communities ◽

Soil Microbial Communities ◽

Microbial Interactions ◽

Field Soil ◽

Next Generation ◽

Giant Ragweed ◽

Generation Sequencing ◽

Rhizosphere Microbial Community

In a previous study, glyphosate-susceptible and -resistant giant ragweed biotypes grown in sterile field soil survived a higher rate of glyphosate than those grown in unsterile field soil, and the roots of the susceptible biotype were colonized by a larger number of soil microorganisms than those of the resistant biotype when treated with 1.6 kg ae ha−1glyphosate. Thus, we concluded that soil-borne microbes play a role in glyphosate activity and now hypothesize that the ability of the resistant biotype to tolerate glyphosate may involve microbial interactions in the rhizosphere. The objective of this study was to evaluate differences in the rhizosphere microbial communities of glyphosate-susceptible and -resistant giant ragweed biotypes 3 d after a glyphosate treatment. Giant ragweed biotypes were grown in the greenhouse in unsterile field soil and glyphosate was applied at either 0 or 1.6 kg ha−1. Rhizosphere soil was sampled 3 d after the glyphosate treatment, and DNA was extracted, purified, and sequenced with the use of Illumina Genome Analyzer next-generation sequencing. The taxonomic distribution of the microbial community, diversity, genera abundance, and community structure within the rhizosphere of the two giant ragweed biotypes in response to a glyphosate application was evaluated by metagenomics analysis. Bacteria comprised approximately 96% of the total microbial community in both biotypes, and differences in the distribution of some microbes at the phyla level were observed. Select soil-borne plant pathogens (VerticilliumandXanthomonas) and plant-growth–promoting rhizobacteria (Burkholderia) present in the rhizosphere were influenced by either biotype or glyphosate application. We did not, however, observe large differences in the diversity or structure of soil microbial communities among our treatments. The results of this study indicate that challenging giant ragweed biotypes with glyphosate causes perturbations in rhizosphere microbial communities and that the perturbations differ between the susceptible and resistant biotypes. However, biological relevance of the rhizosphere microbial community data that we obtained by next-generation sequencing remains unclear.

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Modelling the role of selection and complementarity in ecosystem function under climate change

10.5194/egusphere-egu2020-16475 ◽

2020 ◽

Author(s):

Rebecca Millington ◽

Peter M. Cox ◽

Francisca C. García ◽

Gabriel Yvon-Durocher

Keyword(s):

Climate Change ◽

Temperature Change ◽

Ecosystem Function ◽

Individual Species ◽

Metabolic Theory ◽

Community Function ◽

Using Data ◽

Multiple Species ◽

The Individual

Understanding how ecosystem function depends on temperature is important in understanding ecosystem resilience to climate change. The response to warming at a species level is relatively well understood, through the metabolic theory of ecology, which captures the temperature dependence of biological processes. However, when multiple species are present, interactions between the species are important too. Therefore, to understand community function, we must understand the response of the individual species, and the interactions between them. These interactions may depend on temperature, and can be split into two main mechanisms: selection and complementarity. Both of these processes are likely to depend on the number of species present; the biodiversity of the ecosystem. Currently, the response of communities to temperature change, and how changes in diversity may increase or buffer impacts, is poorly understood. &#160;Our understanding of ecosystem function can be improved by using mathematical models to constrain the mechanisms underlying key processes. Using data from laboratory experiments, we model communities of heterotrophs responding to temperature change. To model selection, we use a simple model of a community sharing a resource, with parameters measured empirically. Without complementarity, the model underestimates community function. Complementarity is included through a single parameter, which determines to what extent different taxa share the same resource pool. This parameter is difficult to measure directly, so must be fitted using empirical community function data. Through our model, we show that the strength of complementarity within a community depends on both diversity and temperature. Interestingly, we also find that complementarity is strongest at higher and lower temperatures, and more dependent on diversity at medium temperatures.

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