Exhibit 10.58

AMENDMENT TO

EMPLOYMENT AGREEMENT

THIS AMENDMENT TO EMPLOYMENT AGREEMENT (the “Amendment”) is effective as of
March 31, 2011 (the “Effective Date”), and as of the Effective Date amends the
Employment Agreement dated April 24, 2009 by and between VERENIUM CORPORATION
(hereinafter the “Company”), and James Levine (hereinafter “Executive”) (the
“Employment Agreement”).

RECITALS

WHEREAS, the Company and Executive wish to amend the Employment Agreement as of
the Effective Date to reflect the Executive’s (1) new duties and
responsibilities as the Company’s President and Chief Executive Officer, and
(2) revised compensation arrangement and other terms of employment;

NOW, THEREFORE, the Company and Executive, in consideration of the mutual
promises set forth herein, agree that the Employment Agreement is amended as of
the Effective Date as follows:

ARTICLE 1

AMENDMENTS

1.1 Section 2. Section 2 of the Employment Agreement is hereby amended and
restated in its entirety as follows:

“2. Duties and Responsibilities. During the Term of this Agreement, you shall
have, and you agree to carry out to the best of your ability, the duties and
responsibilities of President and Chief Executive Officer. You shall have such
executive responsibilities and duties as are assigned by the Board of Directors
of the Company (the “Board”) and are consistent with the positions of President
and Chief Executive Officer. In the performance of your duties and
responsibilities hereunder, you shall regularly report to the Board. You agree
to devote your full business time, attention and energies to the business and
interests of the Company during the Term of this Agreement and you will not
accept any outside position without the prior written consent of the Board,
except that you may serve on up to a maximum of two boards of directors provided
that you have approval of the Board’s Compensation Committee and provided that
your time spent in such service is reasonable and does not detract from the
performance of your duties to the Company. You warrant that you are free to
enter into and fully perform this Agreement and are not subject to any
employment, confidentiality, non-competition or other agreement which would
restrict your performance under this Agreement. As soon as practicable following
the Effective Date, you will be appointed to serve in the class of directors
whose terms expire at the Company’s 2013 annual stockholders’ meeting. In
connection with the termination of your employment by the Company as President
and Chief Executive Officer, you shall resign from the Board effective
simultaneously with the effective date of such termination, unless otherwise
requested by the remaining Board members.

 

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You consent and agree to permanently relocate your primary residence to the San
Diego, California area, which relocation is anticipated will occur sometime on
or around June 2011 (the applicable relocation date is the “Relocation Date”).
From and following the Relocation Date, you shall fulfill your duties and
responsibilities to the Company hereunder primarily from the Company’s office
located in San Diego, California; provided, however, that the Company may from
time to time require you to travel temporarily to other locations in connection
with the Company’s business. You hereby acknowledge that your relocation to the
San Diego, California area does not trigger any right by you to resign your
employment for “Good Reason.””

1.2 Section 3(a). The first sentence of Section 3(a) of the Employment Agreement
is hereby amended and restated in its entirety to read as follows:

“Commencing on the Effective Date, and during the Term of this Agreement, the
Company will pay you a base salary at not less than the biweekly rate of
$15,000.00 (“Base Salary”), minus withholdings as required by law or other
deductions authorized by you, which amount shall be paid to you in periodic
installments in accordance with the Company’s payroll practices then in effect.”

1.3 Section 3(b). The first sentence of Section 3(b) of the Employment Agreement
is hereby amended and restated in its entirety to read as follows:

“For each calendar year during the Term of this Agreement, you will be eligible
to receive an annual performance-based incentive bonus, based upon the
achievement of milestones set by the Board, with a target bonus of 60% percent
of the Base Salary earned during such period (the “Bonus”).”

1.4 Section 3(e). Section 3(e) of the Employment Agreement is hereby amended and
restated in its entirety to read as follows:

“(e) Stock Options and Restricted Stock. The Company granted a stock option to
you on February 24, 2011 to purchase up to 164,491 shares of the Company’s
common stock with an exercise price of $3.31 per share, subject to vesting and
the other terms and conditions set forth in the stock option grant notice and
agreement previously provided to you. All Company stock option and restricted
stock awards previously granted to you shall continue in effect from and
following the Effective Date in accordance with their existing terms. You may be
eligible to receive additional grants of Company stock option and restricted
stock awards in the sole discretion and subject to the approval of the
Compensation Committee of the Board.”

1.5 Section 3(j). A new Section 3(j) is hereby added to the Employment Agreement
as follows:

“(j) Relocation Expenses. The Company agrees to reimburse the reasonable and
customary costs of relocation of your primary residence from Boston,
Massachusetts to

 

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San Diego, California, under terms and conditions to be determined in good faith
and pursuant to the mutual agreement of you and the Company.”

1.6 Effective Date and Term of Amended Employment Agreement. With respect to
application of the amendments to the Employment Agreement that are set forth in
this Amendment, all references to the “Effective Date” contained in the amended
Employment Agreement are with respect to the date of March 31, 2011, and all
references to the “Term” of the Employment Agreement are with respect to the
period of employment commencing on March 31, 2011.

ARTICLE 2

GENERAL PROVISIONS

2.1 Impact of Amendment. Except as expressly amended by this Amendment, the
terms of the Employment Agreement remain in full force and effect.

2.2 Governing Law. The validity, interpretation, construction and performance of
this Amendment and the amended Employment Agreement and the rights of the
parties thereunder shall be interpreted and enforced under the law of the
Commonwealth of Massachusetts.

2.3 Validity. The invalidity or unenforceability of any provision of this
Amendment or the Employment Agreement shall not affect the validity or
enforceability of any other provision of this Amendment or the Employment
Agreement, which shall remain in full force and effect.

2.4 Controlling Document. In case of conflict between any of the terms and
condition of this Amendment and the Employment Agreement herein referred to, the
terms and conditions of this Amendment shall control.

2.5 Executive Acknowledgment. Executive acknowledges (a) that he has consulted
with or has had the opportunity to consult with independent counsel of his own
choice concerning this Amendment, and has been advised to do so by the Company,
and (b) that he has read and understands the Amendment, is fully aware of its
legal effect, and has entered into it freely based on his own judgment.

2.6 Counterparts. This Amendment may be executed in one or more counterparts,
all of which taken together shall constitute one and the same document.

[Remainder of Page Intentionally Left Blank]

 

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Executed by the parties hereto on the date(s) set forth below:

 

 

EXECUTIVE     VERENIUM CORPORATION By:   /s/ James Levine     By:   /s/
Dr. James Cavanaugh   James Levine       Dr. James Cavanaugh         Chairman of
the Board of Directors Date:   March 4, 2011     Date:   March 4, 2011

 

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