Microbial communities and geochemical dynamics in an extremely acidic, metal-rich stream at an abandoned sulfide mine (Huelva, Spain) underpinned by two functional primary production systems

McAllister, T. A., Beauchemin, K. A., Alazzeh, A. Y., Baah, J., Teather, R. M. and Stanford, K. 2011. Review: The use of direct fed microbials to mitigate pathogens and enhance production in cattle. Can. J. Anim. Sci. 91: 193–211. Direct-fed microbials (DFM) have been employed in ruminant production for over 30 yr. Originally, DFM were used primarily in young ruminants to accelerate establishment of the intestinal microflora involved in feed digestion and to promote gut health. Further advancements led to more sophisticated mixtures of DFM that are targeted at improving fiber digestion and preventing ruminal acidosis in mature cattle. Through these outcomes on fiber digestion/rumen health, second-generation DFM have also resulted in improvements in milk yield, growth and feed efficiency of cattle, but results have been inconsistent. More recently, there has been an emphasis on the development of DFM that exhibit activity in cattle against potentially zoonotic pathogens such as Escherichia coli O157:H7, Salmonella spp. and Staphylococcus aureus. Regulatory requirements have limited the microbial species within DFM products to organisms that are generally recognized as safe, such as lactic acid-producing bacteria (e.g., Lactobacillus and Enterococcus spp.), fungi (e.g., Aspergillus oryzae), or yeast (e.g., Saccharomyces cerevisiae). Direct-fed microbials of rumen origin, involving lactate-utilizing species (e.g., Megasphaera elsdenii, Selenomonas ruminantium, Propionibacterium spp.) and plant cell wall-degrading isolates of Butyrivibrio fibrisolvens have also been explored, but have not been commercially used. Development of DFM that are efficacious over a wide range of ruminant production systems remains challenging because[0] comprehensive knowledge of microbial ecology is lacking. Few studies have employed molecular techniques to study in detail the interaction of DFM with native microbial communities or the ruminant host. Advancements in the metagenomics of microbial communities and the genomics of microbial–host interactions may enable DFM to be formulated to improve production and promote health, responses that are presently often achieved through the use of antimicrobials in cattle.

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Copper affects composition and functions of microbial communities in marine biofilms at environmentally relevant concentrations

10.7287/peerj.preprints.27129 ◽

2018 ◽

Author(s):

Natàlia Corcoll ◽

Jianghua Yang ◽

Thomas Backhaus ◽

Xiaowei Zhang ◽

Martin Karl Eriksson ◽

...

Keyword(s):

Community Structure ◽

Primary Production ◽

Microbial Communities ◽

Algal Biomass ◽

Amplicon Sequencing ◽

Quality Standard ◽

Aquatic Communities ◽

Static Test ◽

Community Function ◽

Eukaryotic Organisms

Cu pollution in coastal areas is a worldwide threat for aquatic communities. This study assesses the effects of Cu exposure on microbial diversity, community structure and functions of microbial communities in marine periphyton biofilms at environmental relevant concentrations. Periphyton was exposed for 18 days to five Cu concentrations, between 0.01 and 10 μM, in a semi-static test. Diversity and community structure of prokaryotic and eukaryotic organisms were assessed by 16S and 18S amplicon sequencing, respectively. Community function was studied as impacts on algal biomass and primary production. Additionally, we studied Pollution-Induced Community Tolerance (PICT) using photosynthesis as the endpoint. Sequencing results detected an average of 9504 and 1242 OTUs for 16S and 18S, respectively, reflecting the huge biodiversity of marine periphytic biofilms. Eukaryotes represent the most Cu-sensitive kingdom, where effects were seen already at concentrations as low as 10 nM. The structure of the prokaryotic part of the community was impacted at slightly higher concentrations (60 nM), which is still in the range of the Cu concentrations observed in the area (80 nM).The current environmental quality standard for Cu of 70 nM therefore does not seem to be sufficiently protective for periphyton. Cu exposure resulted in a more Cu-tolerant community, which was accompanied by a reduced total algal biomass, increased relative abundance of diatoms and a reduction of primary production. Cu exposure changed the network of associations between taxa in the communities. A total of 23 taxa, including species within Proteobacteria, Bacteroidetes, Stramenopiles and Hacrobia, were identified as being particularly sensitive to Cu. DNA metabarcoding is presented as a sensitive tool for community-level ecotoxicological studies that allows to observe impacts simultaneously on a multitude of pro- and eukaryotic species, and therefore to identify particularly sensitive, non-cultivable species and taxa.

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Upscaling Gross Primary Production in Corn-Soybean Rotation Systems in the Midwest

Remote Sensing ◽

10.3390/rs11141688 ◽

2019 ◽

Vol 11 (14) ◽

pp. 1688 ◽

Cited By ~ 2

Author(s):

Christian Dold ◽

Jerry L. Hatfield ◽

John H. Prueger ◽

Tom B. Moorman ◽

Tom J. Sauer ◽

...

Keyword(s):

Land Use ◽

Primary Production ◽

Production Systems ◽

Ecosystem Respiration ◽

Meteorological Data ◽

Gross Primary Production ◽

Corn Yield ◽

Yield Data ◽

Carbon Dioxide Fluxes ◽

Land Use Maps

The Midwestern US is dominated by corn (Zea mays L.) and soybean (Glycine max [L.] Merr.) production, and the carbon dynamics of this region are dominated by these production systems. An accurate regional estimate of gross primary production (GPP) is imperative and requires upscaling approaches. The aim of this study was to upscale corn and soybean GPP (referred to as GPPcalc) in four counties in Central Iowa in the 2016 growing season (DOY 145–269). Eight eddy-covariance (EC) stations recorded carbon dioxide fluxes of corn (n = 4) and soybean (n = 4), and net ecosystem production (NEP) was partitioned into GPP and ecosystem respiration (RE). Additional field-measured NDVI was used to calculate radiation use efficiency (RUEmax). GPPcalc was calculated using 16 MODIS satellite images, ground-based RUEmax and meteorological data, and improved land use maps. Seasonal NEP, GPP, and RE ( x ¯ ± SE) were 678 ± 63, 1483 ± 100, and −805 ± 40 g C m−2 for corn, and 263 ± 40, 811 ± 53, and −548 ± 14 g C m−2 for soybean, respectively. Field-measured NDVI aligned well with MODIS fPAR (R2 = 0.99), and the calculated RUEmax was 3.24 and 1.90 g C MJ−1 for corn and soybean, respectively. The GPPcalc vs. EC-derived GPP had a RMSE of 2.24 and 2.81 g C m−2 d−1, for corn and soybean, respectively, which is an improvement to the GPPMODIS product (2.44 and 3.30 g C m−2 d−1, respectively). Corn yield, calculated from GPPcalc (12.82 ± 0.65 Mg ha−1), corresponded well to official yield data (13.09 ± 0.09 Mg ha−1), while soybean yield was overestimated (6.73 ± 0.27 vs. 4.03 ± 0.04 Mg ha−1). The approach presented has the potential to increase the accuracy of regional corn and soybean GPP and grain yield estimates by integrating field-based flux estimates with remote sensing reflectance observations and high-resolution land use maps.

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Primary production of freshwater microbial communities is affected by a cocktail of herbicides in an outdoor experiment

Ecotoxicology and Environmental Safety ◽

10.1016/j.ecoenv.2020.110821 ◽

2020 ◽

Vol 201 ◽

pp. 110821

Author(s):

V.L. Lozano ◽

S. Allen Dohle ◽

M.S. Vera ◽

A. Torremorell ◽

H.N. Pizarro

Keyword(s):

Primary Production ◽

Microbial Communities ◽

Outdoor Experiment

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Soil microbial communities in tilled organic and no-till conventional crop production systems

Organic Agriculture ◽

10.1007/s13165-021-00360-4 ◽

2021 ◽

Author(s):

Newton Z. Lupwayi ◽

Cynthia A. Grant ◽

John T. O’Donovan ◽

Andrea H. Eastman ◽

Greg Semach ◽

...

Keyword(s):

Microbial Communities ◽

Crop Production ◽

Production Systems ◽

Soil Microbial Communities ◽

Soil Microbial ◽

No Till

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Sea ice microbial communities. VI. Growth and primary production in bottom ice under graded snow cover

Marine Ecology Progress Series ◽

10.3354/meps035153 ◽

1987 ◽

Vol 35 ◽

pp. 153-164 ◽

Cited By ~ 91

Author(s):

SM Grossi ◽

ST Kottmeier ◽

RL Moe ◽

GT Taylor ◽

CW Sullivan

Keyword(s):

Sea Ice ◽

Primary Production ◽

Microbial Communities ◽

Snow Cover

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Utilizing principles of Biodiversity Science to Guide Soil Microbial Communities for Sustainable Agriculture

10.32942/osf.io/tm5eh ◽

2021 ◽

Author(s):

Seraina Lisa Cappelli ◽

Luiz Domeignoz Horta ◽

Viviana Loaiza ◽

Anna-Liisa Laine

Keyword(s):

Microbial Communities ◽

Plant Diversity ◽

Ecosystem Functioning ◽

Production Systems ◽

Soil Microbial Communities ◽

Empirical Support ◽

Soil Biodiversity ◽

Sustainable Food ◽

Soil Microbial ◽

Below Ground

While the positive relationship between plant biodiversity and ecosystem functioning (BEF) is relatively well-established, far less in known about the extent to which this relationship is mediated via below-ground microbial responses to plant diversity. Limited evidence suggests that the diversity of soil microbial communities is sensitive to plant community structure, and that diverse soil microbial communities promote functions desired of sustainable food production systems such as enhanced carbon sequestration and nutrient cycling. Here, we discuss available evidence on how plant diversity could be utilized to purposefully guide soil biodiversity in agricultural systems that are typically depleted of biodiversity, and are notoriously sensitive to both biotic and abiotic stressors. We outline the direct and soil microbe-mediated mechanisms expected to promote a positive BEF relationship both above- and below-ground. Finally, we identify management schemes based on ecological theory and vast empirical support that can be utilized to maximize ecosystem functioning in agroecosystems via biodiversity implementation schemes.

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Microdiversity characterizes prevalent phylogenetic clades in the glacier-fed stream microbiome

The ISME Journal ◽

10.1038/s41396-021-01106-6 ◽

2021 ◽

Author(s):

Stilianos Fodelianakis ◽

Alex D. Washburne ◽

Massimo Bourquin ◽

Paraskevi Pramateftaki ◽

Tyler J. Kohler ◽

...

Keyword(s):

New Zealand ◽

Primary Production ◽

Microbial Communities ◽

Analytical Framework ◽

Α Diversity ◽

High Prevalence ◽

Ecological Success ◽

Underlying Mechanisms

AbstractGlacier-fed streams (GFSs) are extreme and rapidly vanishing ecosystems, and yet they harbor diverse microbial communities. Although our understanding of the GFS microbiome has recently increased, we do not know which microbial clades are ecologically successful in these ecosystems, nor do we understand potentially underlying mechanisms. Ecologically successful clades should be more prevalent across GFSs compared to other clades, which should be reflected as clade-wise distinctly low phylogenetic turnover. However, methods to assess such patterns are currently missing. Here we developed and applied a novel analytical framework, “phyloscore analysis”, to identify clades with lower spatial phylogenetic turnover than other clades in the sediment microbiome across twenty GFSs in New Zealand. These clades constituted up to 44% and 64% of community α-diversity and abundance, respectively. Furthermore, both their α-diversity and abundance increased as sediment chlorophyll a decreased, corroborating their ecological success in GFS habitats largely devoid of primary production. These clades also contained elevated levels of putative microdiversity than others, which could potentially explain their high prevalence in GFSs. This hitherto unknown microdiversity may be threatened as glaciers shrink, urging towards further genomic and functional exploration of the GFS microbiome.

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