NIMBioS Investigative Workshop Individual-Based Ecology of Microbes: Observations and Modeling June...

NIMBioS Investigative Workshop

Individual-Based Ecology of Microbes: Observations

and Modeling

June 8-10, 2011

Knoxville, Tennessee

Q3: Interactions with the environment

Elucidating the bacteria responsible for

utilization of dissolved organic matter in

streams

Philips Akinwole

Personal Introduction

MSc in Environmental Science and Technology (2003-2005)

International Institute for Infrastructural, Hydraulic,

and Environmental Engineering, (UNESCO-IHE), Delft, the Netherlands

Project: Litter decomposition across multiple spatial scales in German stream

networks

so…I’m broadly trained in stream and microbial ecology using

stable isotope

probing and phospholipid techniques (a multidisciplinary

approach) to link

microbial community structures to functions

… presentlyPhD Candidate in Microbial Ecology/ Department of Biological Sciences

University of Alabama, Tuscaloosa, AL (2007…)

… interested in linking microbial community structures

to functionsPresenting Projects:

Stable Isotope Probing of Dissolved Organic Matter Processing in

Streams

Spatial Patterns of Microbial Signature Biomarkers in Stream Networks

Measuring dissolved organic matter spiraling lengths: whole stream

releases

Elucidating the bacteria responsible for utilization of dissolved organic matter in streams

Streams and rivers can be found everywhere.

Bodies of flowing water moving in one direction from

headwaters

(springs, snowmelt or even lakes) and then travel all

the way to

their mouths, usually another water channel or the

ocean.

The characteristics of a river or stream change

during the journey

from the source to the mouth.

Full of life; from microbes to plants (algae and

macrophytes) and

animals (fish and macroinvertebrates).

… some concepts

Dissolved organic matter (DOM), the largest pool of carbon in

aquatic ecosystems, is heterogeneous in nature and supplies the

needed energy and carbon to microbes; in streams it may meet

the majority of heterotroph carbon demand (Kaplan et al.,

2008).

…bacterial are the main heterotrophic microorganisms in stream

responsible for the breakdown of organic biomass and the

recycling of various key elements (N,P,S,C)

Neversink River,

NY


One of the methods (biochemical and molecular) of studying

microbial diversity/community structure is the Phospholipid

Fatty Acid (PLFA) Analysis PLFAs are a major component of the cell membrane of

all microbes

(bacteria and eukaryotes) and they only remain intact

in viable cells.

are relatively easily extracted from natural samples.

PLFA analysis as biomarkers provides direct

information on the

whole microbial community including quantitative

information

on viable (living) biomass, community structure

(Population

“Fingerprint”) and microbial activity.

Fatty acids are identified and quantified

by gas chromatograph (GC).


Stable Isotope Analysis

Isotopes are forms of an element that differ in the number of neutron (H, C,

N, O & S)

- functions as natural dyes/colors, generally tracking the circulation of

elements

(discrimination between heavy and lighter isotopes).

-- trace ecological connections at many levels, from individual microbes to

whole landscapes

Direct links between microbial identity and biogeochemical processes

are now possible with stable isotope analysis of biomarkers (lipids,

amino acids & nucleic acids)Usually, stable isotope ratios are given in the δ-notation,which for carbon is defined as:

… measured with the gas chromatography-combustion-isotope ratio mass spectrometry (GC/C/IRMS).

In stream ecosystems, monomeric constituents of DOM are

most labile while polymeric /humic substances of

terrestrial origin are the major constituents of DOM pool

(40-70% of DOM in rivers) and have been considered

biochemically refractory (Benner 2003)

… and poorly used by microbiota due to the apparent

chemical recalcitrance of humic substances.


Recent studies (Frazier et al.2005, Kaplan et al.,

2008 etc) have suggested the susceptibility of

humic substances to microbiological and photolytic

oxidations and could provide a supplement to

heterotrophic metabolism.

This study was framed within the general question “Does

streamwater DOM contribute significantly to stream ecosystem

metabolism?” and particularly addressed the question

“Which microorganisms within the stream community utilize

humic-DOM?”


-generate a tracer model that is more reflective

of natural stream DOM, contrasting the use of

bicarbonate or acetate as tracers (e.g. Pace et

al., 2004; Johnson & Tank 2009),

- we synthesized a 13C-DOM tracer from tulip

poplar tree-tissues with size and lability

fractions approximating streamwater DOM

(Wiegner et al., 2005).

…to do this

min24 26 28 30 32 34 36 38

pA

0

100

200

300

400

500

600

700

FID1 B, (CHYTRID1\RI.D)

24.126

26.706

28.568

28.814

29.244

30.335 30.48

1 30.77

2 30.90

6 31.06

6 31.545

32.553

32.620

32.741

32.940

33.207

33.300

33.805

35.286

36.816

36.899

39.427


… research activities

Collection of

streambed

sediment from

WCC

Sediments were

incubated in

mesocosm

chambers with

175 µg C L-1 13C –

labeled DOM

Microbial biomass

and community

structure were

analyzed by PLFA

The fatty acid methyl esters (FAMEs)

obtained from PLFA analyses were

identified and quantified by GC, and

analyzed for their δ13C values using the

GC-IRMS.

For each experiment , treatments were identified as:

T0 – sediments collected from WCC at the beginning of the experiments;

T13C – sediments incubated for 48hrs in streamwater amended with 13C-

labeled leachate and,

T50 – sediments incubated for 48hrs in streamwater.

Four experiments were conducted in the light (unfiltered

sunlight) and dark (chambers were covered with styrofoam

and black plastic)

Results


br17:1a, a17, 18:1w5, i17, cy17:0, br18:0a, 10me16, i16, cy19, a15

22:6w3, 16:1w13t, 20:5w3, 16:3, 20:4w6, br18:0c, 14:0

16:1w7c br17:0, 16:4w1

17:0, 22:0, br19:1a, 20:0, 18:0, 18:1w9

PCA to evaluate changes in total microbial community structure during mesocosm incubation. Red arrows emphasize a comparison between T0 and T48/50 data (mesocosm controls) while blue arrows emphasize a comparison between T0 and T13C data (13C-DOM treatment).

[● (Exp1), ♦ (Exp 2), ▲(Exp3), ■ (Exp4)]

Results

i15

a15

16 c

lust

er*

16:0

10m

e16

cy17,c

oelu

ter

18 c

lust

er*

cy19

20 c

lust

er*

21:0

, 22:6

w3

-45

-40

-35

-30

-25

T0/ Exp1 T48/Exp1 T13C/Exp1

PLFAs

δ13C

valu

e (

‰)


Stable carbon isotopic information for PLFAs from Experiment 1 (Dark) sediment incubated with and without 13C-labelled DOM

T0 = natural stream sediments T48 = natural steam sediments incubated with recirculating streamwater for 48 hrs T13C = natural steam sediments incubated with recirculating streamwater amended with 13C-DOM for 48hrs

FAME Bio marker EXP 1 (Dark)

EXP 2 (Light)

EXP 3 (Light)

EXP 4 (Light)

i15:0 Prokaryote √ √ √ √

a15:0 Prokaryote √ X √ √

16:0 Non specific √ √ √ √ 16:1w7c,

16:1w5c Prokaryote √ Depletion √ √

16:1w9 Non specific √ √ √ √

10me16:0 Prokaryote X X X X

cy17:0 Prokaryote √ X X X

18:2w6 Eukaryote X X ? X

18:3w3 Eukaryote √ X ? X 18:1w9c,

18:1w7c Non specific √ √ √ √

cy19:0 Prokaryote √ X X X

20:4w6 Eukaryote √ X ? ?

20:5w3 Eukaryote √ √ √ X

22:6w3 Eukaryote √ X X X

√= Enrichment X = No enrichment ? = Potential enrichment

Summary of incorporation of 13C-labeled DOM into microbial lipid by experiment

Results

Incorporation of label into PLFA was studied in light and dark

incubations .

Dark incorporation was fully sensitive to 13C-labelled DOM

utilization

Conclusions

The PCA analysis of microbial biomass and community structure validate the

robustness of

mesocosm-based experimental design for determining the role of sediment

microbes in

processing streamwater DOM via incorporation of 13C-DOM into microbial

fatty acids.

PLFA analysis indicated that both phototrophic and heterotrophic

microeukaryotes were

present in the sediment community. For the dark experiment, we assume

that the

13C- labeled DOM uptake by prokaryotes is direct and not facilitated by

photolysis.

The consistently labeled fatty acids: i15:0. 16:0, 16:1w9, 18:1w9c and 18:1w7c

in our

study are found in bacteria often associated with aerobic or facultative

anaerobic

metabolism (Findlay 2004).

Fatty acids 10me16:0 (showed no labeling) and cy17:0 (only showed

moderately labeling

when sediments were incorporated in the dark) are consistently found in

bacteria

associated with anaerobic metabolism, such as sulfate reducing bacteria.

Eukaryotic marker fatty acids (20:4w6, 20:5w3) were most constantly labeled

in the dark

experiment suggesting that microeukaryotic predators are consuming

bacteria utilizing

13C-labeled DOM.

… motivation for and challenges in individual base approach

Individual based approach use information at the level of individual organisms and derive characteristics of the population as an integral of all individuals represented in the population.

- Successfully applied in conservation biology

…however, they include many parameters which are difficult to estimate for natural populations and which rely on very detailed knowledge on the species and the spatial structure of its populations.

- I’m interested in how to apply/use individual base model in my work, - advances made in microbial ecology, - applications and uses in other areas

Thank you

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